VEGA

Molecular Modeling Toolkit

Printable manual

1. Introduction

VEGA was developed to create a bridge between most of the molecular software packages, as Quanta/CHARMm, Insight II, Mopac, etc. In this tool, some features have been implemented to analyze and manage 3D structures of molecules. VEGA is written in high portable code (standard C language) and can be executed on a lot of hardware systems simply recompiling the source code. The program is already tested on the following operating systems: IRIX (Silicon Graphics), Windows 9x/NT/2000/XP/Vista/7/8 PCs, Linux, FreeBSD, NetBSD, AmigaOS, etc.

The most significant features implemented in VEGA are:

• Supported input file formats: Alchemy, AMMP, Accelrys Insight .car and .arc, Accelrys Quanta/CHARMm CRD, AutoDock 4 PDBQT, AutoDock Vina PDBQT, CSR, MSF and DCD, CML 1.0 and 2.0, BioDock output, Cambridge Data File (CSSR), Chem3D, ChemDraw CDX, ChemSol, Cartesian coordinates (XYZ), CPMD XYZ, EMPIRE .arc and .dat, ESCHER NG solutions, GAMESS cartesian input and output, Gaussian cartesian input and output,  GRAMM solutions, Gromos/Gromacs .gro and .xtc, HyperChem .hin, InChI, Interchange File Format (IFF/RIFF), IUCr Crystallographic Information Framework (CIF, mmCIF), IUMSC CRT, LiGen binary/text pocket, MDL Molfile, Mopac cartesian coordinates, Mopac internal coordinates, Mopac Guassian Z-matrix, NAMD binary, Protein Data Bank (PDB), Data Bank with ATDL atom types (PDBA), Protein Data Bank Fat (PDBF), PQR, PQR XML, Protein Data Bank MultiModel, QMC, SMILES, Spillo RBS, TINKER XYZ, Tripos Sybyl (Mol2), X-Plor PSF.

• Supported output file formats: Accelrys Insight .car (archive 1 and 3), Accelrys Quanta/CHARMm CRD and MSF, Alchemy, AMMP, AutoDock 4 PDBQT, AutoDock Vina PDBQT, Cambridge Data File (CSSR), Cartesian coordinates (XYZ), ChemSol, CML 1.0 and 2.0, CPMD XYZ, Crystallographic Information Framework for macromolecules (mmCIF), Fasta, GAMESS cartesian, Gaussian cartesian input, Gromos/Gromacs .gro, InChI, InChI Aux, Interchange File Format (IFF), IUCr Crystallographic Information Framework (CIF), IUMSC CRT, MDL Molfile, Mopac cartesian coordinates, Mopac internal coordinates, NAMD binary, Protein Data Bank (PDB), Protein Data Bank with ATDL atom types (PDBA), Protein Data Bank with atomic charges (PDBQ), Protein Data Bank Fat (PDBF), Protein Data Bank with more than 99999 atoms (PDBL), Protein Data Bank simplified, PQR, PQR XML, SMILES, Spillo RBS, Tripos Sybyl (Mol2), VRML.

• Supported output surface formats: CSV,  IFF/RIFF, Insight, Quanta, raw binary, VRML.

• Supported output trajectory formats: Charmm DCD,  IFF/RIFF, Mol2 multi-model, PDB multi-model, Gromacs TRR and Gromacs XTC.

• Atomic charge attribution by Gasteiger method or a template of residues.

• Atom type attribution. The supported atom types are: AM1BCC, AMBER, AutoDock, Bond, Broto/Moreau (BROTO), CFF91, CHARMm, CHARMM 22 for nucleic acids (CHARMM22_NA), CHARMM 22 for lipids (CHARMM22_LIPID), CHARMM 22 for proteins (CHARMM22_PROT), CHARMM 36 (CHARMM36_GEN), CVFF, Ghose/Crippen (CRIPPEN), Ghose/Crippen for molar refractivity (CRIPPEN_MR), functional groups (GROUPS), GRID, H-bond (HBOND), logS, Meng, MM+, MM2, MM3, MMFF, Tripos, UNIV and any other user defined template. A simple language to define the atom types is built-in (ATDL).

• Calculation of molecular surfaces (Van der Waals, accessible to solvent, Molecular Electrostatic Potential (MEP), Molecular Hydropathicity Index (ILM) and Virtual logP (MLP)).

• Capability to add the hydrogens.

• Calculation of ligand-receptor interaction energy for each residue involved in the binding.

• Evaluation of logP (Broto/Moreau, Ghose/Crippen, Virtual logP) and lipole (Broto/Moreau, Ghose/Crippen).

• Evaluation of the molecular refractivity (Ghose/Crippen method).

• Analysis of MD trajectories. VEGA can read: Accelrys archive file (.arc), AutoDock 4 DLG, BioDock output, CSR (Accelrys conformational search), DCD, ESCHER NG, GRAMM, Gromacs TRR, Gromos XTC, IFF/RIFF (32 and 64 bit), Crystallographic Information Framework multi-model (CIF, mmCIF), MDL Mol multi-model, Merck MMD, Tripos Mol2 multi-model, PDB multi-model and PDBQT multi-model file formats. It's possible to calculate several properties as the interatomic distance, the bond angle, the torsion, the angle between two planes, the molecular surface, the surface diameter, the molecular volume, the volume diameter, the dipole, the Virtual logP.

• Molecule extraction from databases (IUPAC names, Microsoft Access, Merck MMD, Mol2, ODBC, SMILES, Sdf, SQLite and Zip).

• Coordinates normalization.

• Molecule solvation with any type of cluster.

• Deletion of water molecules and hydrogen atoms.

• Residue renumbering.

• OpenCL acceleration for both Windows and Linux versions.

2. Installation

The VEGA package is available in different archives/setups:

where X.X.X and X.X.X.X are the release version of each archive/setup. You you can download only the package for your system, because each archive contains all the files needed, but not the source code that is provided in a separate archive.

2.1 Unix installation

This section of the manual shows the steps needed to install the VEGA package on Unix-like operating systems (e.g. IRIX, Linux, NetBSD, etc). If your operating system is not directly supported by Authors, you must download and compile the source code (Vega_X.X.X_Source.tar.gz archive).

2.1.1 Building the VEGA package

The portable source code allows to build the package virtually for any computer platform that has a standard ANSI C compiler. It is possible to find some minor compiling problems due to hardware differences. If you can't solve these problems, please contact the Authors.

As first step, you must unpack the Vega_XX_Source.tar.gz file, using the gzip command. If this command is not available in your system, you can download it from any GNU software archive (see: http://www.opensource.org). The correct syntax is:

gzip -d Vega_X.X.X_Source.tar.gz

the unpacked file (Vega_X.X.X_Source.tar) created by gzip must be dearchived with tar command:

tar -xvf Vega_X.X.X_Source.tar

A directory called Vega will be created.

Check if the libraries libbz2.a, loblocale.a, libxdrf.a, libz.a and libZ32.a are present in the directory ...Vega/Src/Vega/MySO where MySO is the directory of your operating system. If not, you must compile these external libraries using the sources placed respectively in ...Vega/Src/Bzip2, ...Vega/Src/LocaleLib, ...Vega/Src/XdrfLib, ...Vega/Src/Zlib and ...Vega/Src/Z32 editing the Makefile and running make. Each library must be copied in ...Vega/Src/Vega/MySO.

After this operation, change your current directory in ...Vega/Src/Vega/MySO (Amiga, Irix, Linux, Unix, Win32) and, if needed, edit the Makefile with your preferred program. Some remarks can help you in this operation. Please set the CC variable to the compiler name (usually cc or gcc) and the CFLAGS variable for the best optimization (e.g. -O -s).

At this point, run make and the VEGA executable is compiled for your system. The makefile was successfully tested with SGI cc and GNU C (gcc for Linux, gcc for AmigaDOS) compilers.

WARNING:
Starting from the 1.5.0 release, it was introduced the use of 64 bit integers to speed-up the manipulation of 8 character strings and thus to build VEGA, it's required a C compiler that supports that integer size. 

2.1.2 Setting-up your Unix system

If the downloaded package has been specifically developed for your operating system, you must unpack it using the following two commands:

gzip -d Vega_X.X.X_MyOS.tar.gz

tar -xvf Vega_X.X.X_MyOS.tar

If you have GNU tar, you can even do it in one step only:

tar -zxvf Vega_X.X.X_MyOS.tar.gz

Please note that the pathway where the archive has been unpacked, is the real installation path.

Test installation

Type the command (one time only):

chmod -R 755 Vega/Bin/*

and every time that you need VEGA:

cd Vega
source ./assign.sh

In this way, the more suitable set of binaries is automatically detected and its folder is added to the command search path.

Full installation
The next step is the editing of your shell start-up script (e.g. .cshrc for csh or tcsh, .bashrc for GNU bash) in order to set VEGADIR and the LD_LIBRARY_PATH environment variables to the installation path. For csh/tcsh shell, you must type:

setenv VEGADIR "<INSTALLATION_PATH>"
setenv LD_LIBRARY_PATH "$VEGADIR/Bin/<MyOS> $LD_LIBRARY_PATH"
setenv PATH "$VEGADIR:$PATH"

where <MyOS> is the operating system  (e.g. Linux_x64, Linux_x86, etc) and  <INSTALLATION_PATH> is the full installation path.

For sh/bash:

export VEGADIR="<INSTALLATION_PATH>"
export LD_LIBRARY_PATH="$VEGADIR $LD_LIBRARY_PATH"
export PATH="$VEGADIR/Bin/<MyOS>:$PATH"

The LD_LIBRARY_PATH is required to inform your system where are the dynamic libraries needed by VEGA. It's strongly recommended to add the installation directory pathway in the command search variable path, defined in shell start-up script.

For example, if you installed VEGA for Linux x64 in /usr/local/vega directory, you must set the environment variables (csh/tcsh):

setenv VEGADIR "/usr/local/vega"
setenv LD_LIBRARY_PATH "$VEGADIR $LD_LIBRARY_PATH"
setenv PATH "$VEGADIR/Bin/Linux_x64:$PATH"

or (sh/bash):

export VEGADIR="/usr/local/vega"
export LD_LIBRARY_PATH="$VEGADIR $LD_LIBRARY_PATH"
export PATH="$VEGADIR/Bin/Linux_x64:$PATH"

Finally, you must change the file permissions:

chmod -R 755 $VEGADIR/Bin

To set the localization language of VEGA program, you can edit the <INSTALLATION_PATH>/Config/prefs file: find the <LANGUAGE> item and select your preferred language (at this time, two languages are supported only: english and italian). The automatic language selection isn't supported by Unix operating systems. The installation can be completed enabling the OpenCL acceleration, if the host operating system is Linux x86/x64.

2.1.2 Linux and OpenCL

If your system is equipped with an OpenCL-enabled device (a GPU or an accelerator) and its driver is correctly installed, VEGA recognizes and uses it automatically. For AMD GPUs (HD4000 series and above) and for systems not equipped with a OpenCL-ready GPU, you must install the ATI Stream SDK. In the second case, the OpenCL acceleration is available even if a compatible GPU is not installed, by the CPU that must support SSE2 instruction set to emulate the OpenCL environment. Although the performance aren't comparable to a real OpenCL device, you can obtain a speed-up due to the massive use of the SIMD instructions by the real-time OpenCL compiler.

To install the ATI Stream SDK:

• go to ATI Stream SDK download page and choose the most appropriate version for your system (Linux 32 or 64 bit);
• with the mministrative rights, download and unpack it in the directory in which it will be installed:

tar -xvzf ati-stream-sdk-vX.X-lnxYY.tgz

where X.X is the SDK version and YY could be 32 or 64 on the basis of the version chosen by you. Remember that the examples and the C includes aren't required by VEGA and if you don't want to develop OpenCL application, you can remove the docs, include, make and samples directories to shrink the installation.

• in your .bashrc file set the following environment variables:

export ATISTREAMSDKROOT=<location where the SDK is installed>
export ATISTREAMSDKSAMPLESROOT=$ATISTREAMSDKROOT # Required if you want build the examples

For 32-bit systems:

export LD_LIBRARY_PATH=$ATISTREAMSDKROOT/lib/x86:$LD_LIBRARY_PATH

For 64-bit systems:

export LD_LIBRARY_PATH=$ATISTREAMSDKROOT/lib/x86_64:$LD_LIBRARY_PATH

• If you installed an AMD OpenCL compatible GPU and you want to use both GPU and CPU (not at the same time), you must register the OpenCL ICD driver. To do it, download the package icd-registration.tgz and type in the command shell (with the amministrative rights):

cd /
tar -xvzf icd-registration.tgz

If you have a Nvidia OpenCL enabled graphic card (GeForce 8 series and above with at least 256 Mb of ram), download and install the latest CUDA Toolkit for Linux.

If you find any problem using the OpenCL acceleration, see the prefs file in the Data directory to enable/disable or to select devices.

2.2 Windows installation

This release contains two versions: the console (command line) and the ZZ (OpenGL) versions. The first one is a true Win32 console application. It supports long filenames and works fine with Windows 2000, XP, Server 2003, Vista, Server 2008 and 7 operating systems (x86 and x64 editions). The package has been compiled using the standard Pentium Pro ® (686) instruction set. The second version is a powerful application with an enhanced graphic interface. For more information, go to VEGA ZZ section.
To install the Vega_ZZ_XX_Setup.exe package, you must execute this file and follow the simple installation wizard. You must remember that you must have the administrator rights to complete the installation.
If your system has a software firewall, you must configure it granting the network access to REBOL.exe, otherwise the scripting system doesn't work because it uses the standard TCP/IP communication ports.
After the installation, run VEGA ZZ and the activation procedure starts. The setup can be completed installing the optional components and enabling the OpenCL acceleration.

2.2.1 Windows and OpenCL

As explained in the Unix/Linux installation section, if your system is equipped with an OpenCL-enabled device (a GPU or an accelerator) and its driver is correctly installed, VEGA and VEGA ZZ recognize and use it automatically. For AMD GPUs (HD4000 series and above) the OpenCL driver is included in the standard driver package. For the systems not equipped with a OpenCL-ready GPU, you can install ATI Stream SDK which provides the OpenCL acceleration emulated by the CPU that must support SSE2 instruction set. Although the performance aren't comparable to a real OpenCL device, you can obtain a speed-up due to the massive use of the SIMD instructions by the real-time OpenCL compiler.

To install the ATI Stream SDK:

• go to ATI Stream SDK download page and choose the most appropriate version for your system (Windows XP 32/64 bit, Windows Vista/7 32/64 bit);
• run ati-stream-sdk-vX.X-OS.exe where X.X is the SDK version and OS is the chosen operating system. The SDK will be unzipped in the setup directory that you selected;
• if you don't intend to develop OpenCL application, you could perform a custom installation, unchecking all components keeping checked ATI Stream SDK v2 Developer only.

If you have a Nvidia OpenCL enabled graphic card (GeForce 8 series and above with at least 256 Mb of ram), download and install the latest CUDA Toolkit for Windows.

If you find any problem using the OpenCL acceleration, see the Preferences window to enable/disable or to select devices.

2.3 AmigaDOS installation

System requirements needed to run the AmigaDOS version of VEGA:

• AmigaOS 2.04 or greater (3.0 recommended);
• Ixemul.library. If this library is not installed, you can find it in the Aminet archive or Geek Gadgets archive;
• PowerPacker.library (optional for data decompression);
• FPU is strongly recommended, but not required.

To install this version of VEGA package, you must unpack the distribution archive using lha command from the command shell:

lha x Vega_XX_Amiga.lha

A directory called Vega will be automatically created. If you don't have lha, you can download it from Aminet. As for Unix systems, you must add in the user-startup file (placed in s directory of your boot disk) the following line:

SetEnv VEGADIR <INSTALLATION_PATH>

Instead of the user-startup modification, you can create a new text file in ENVARC: directory containing a single line with the installation pathway. Starting from 1.2 release, this installation step is needed only if VEGA executable is placed in a directory that is not the installation folder.

If you want to add VEGA to your standard command pathway, you can add in the user-startup the following line:

Path <INSTALLATION_PATH> Add

As final step, reboot your computer. Please note that VEGA for Amiga can accept AmigaDOS and Unix-like pathway specification. Use the specific VEGA version for the CPU installed in your system:

The PowerPC CPUs aren't supported.

3. Usage

Running the program without parameters, the list of the implemented options is shown:

VEGA 3.2.3 - (c) 1996-2023, Alessandro Pedretti & Giulio Vistoli
Virtual logP by Bernard Testa et al.
Windows x64 (64 bit) version

Synopsis: vega INPUT ... -o[OUT.PACK] -f[OUTPUT_FORMAT] -p[FORCE_FIELD]
          -s[POINTS] -g[RADIUS] -c[TEMPLATE] -k[KEYWORDS] -a[RES_NUM]
          -d[DIELECTRIC] -e[MOLNUM] -i[SHELL RAD SHAPE]-j[TORSIONS]
          -l[MOLTYPE] -m[KEYWORDS] -q[METHOD] -r[MODE] -t[SECSTRUCT]
          -v[CPUS] -x[MODE (ID)] -z[NTERM CTERM] -0bhnuwy
 

0 -> ignore locale settings of the decimal separator
a -> renumber residues starting from RES_NUM
b -> don't save the connectivity
c -> charge template (FORMAL, GASTEIGER, ...)
d -> dielectric constant for energy calculation
e -> molecule number for score calculation (0 = last)
f -> output format
g -> probe radius for SAS
h -> show this help
i -> solvate the molecule
j -> define the torsions (ALL, AUTODOCK, FLEX)
k -> keywords for InfoXML and MopInt
l -> add hydrogens (GEN, GENBO, NA, NABO, PROT, PROTBO)
m -> keywords for trajectory analysis
n -> normalize coordinates
o -> output file name
p -> define force field to apply
q -> fix the bond order (ALL, RINGS)
r -> remove hydrogens (ALL, APOLAR)
s -> point density for SAS
t -> change the protein secondary structure
u -> add the side chains to a protein
v -> number of CPUs (0 = all)
w -> remove waters
x -> list/extract molecule/s from a database (LIST; NAME name; NUM number)
y -> find the molecules in the assembly
z -> N-term and C-term capping for peptide (default: NONE NONE)

INPUT formats:
 Alchemy, AMMP, Arc, AutoDock 4 DLG, BioDock, CAR, CHARMM CRD, CIF, CML,
 CML 2.0, CPMD XYZ, CRT, CHARMM DCD, Chem3D, ChemDraw CDX, ChemSol, CSSR,

 EMPIRE, ESCHER NG, Fasta, GAMESS, Gaussian In/Out, GRAMM, Gromacs/Gromos

 mol, Gromacs TRR, Gromacs XTC, HIN, IFF, InChI, LiGen pocket, MDL,

 MDL V3000, Mol2, Mopac cartesian, Mopac Gaussian Z-matrix, Mopac internal,

 MSF, NAMD binary, PDB, PDBA, PDBF, PDBL, PDBQT, PQR, PQRXML, PSFX, QMC,

 Quanta CSR, RIFF, SDF, TINKER XYZ, XYZ, ZIP.

OUTput formats:
 Calc:       Info, InfoXML, Score.
 Map:        BiosymSrf, ComfaFld, CsvIlm, CsvLogP, CsvMep, CsvSrf,
             QuantaIlm, QuantaLogP, QuantaMep, QuantaSrf.
 Molecule:   Alchemy, AMMP, Biosym, ChemSol, CIF, CML, CML2, CPMDXYZ, CRD,
             CRT, CSSR, Fasta, GAMESS, GaussIn, Gromos, GromosNm, IFF,
             InChI, InChIAux, InChIKey, Indigo, MdlMol, MdlMol3, mmCIF,

             Mol2, MopCar, MopInt, MSF, NamdBin, OldBiosym, PDB, PDB2,

             PDBQ, PDBA, PDBF, PDBL, PDBNOTSTD, PDBQT, PQR, PQRXML,
             PSFX, QMC, RIFF, SMILES, SpilloRBS, VINA, XYZ.
 Plot:       BinPlt, CSV, QuantaPlt.
 Trajectory: TrjDCD, TrjIFF, TrjMol2, TrjPDB, TrjTrr, TrjXtc.
 VRML:       Vrml, VrmlPts, VrmlCpk, VrmlSol.

PACKer formats:
 bz2 (BZip2), gz (GZip), pp (PowerPacker), z (Z-Compress).

Score functions (-f Score -k):
 Broto, Broto2, Broto3, Charmm, Charmm22, Charmm36, CVFF, Elect, ElectDD.

TRAJECTORY keywords (-m):
 Angle A1 A2 A3, Dipole, Distance A1 A2, Extract F1 [F2], GyrRad, ILM,
 LipoleBr, LipoleCr, Ovality, PlaneAng A1 A2 A3 A4 A5 A6, PSA, RMSD,
 RMSDH, RMSDALN, RMSDALNH, RMSDSYMCOR, RMSDSYMCORH, Surface A1 ...,

 SurfDia A1 ..., Torsion A1 A2 A3 A4, VlogP, VolDia, Volume.

Secondary structure keywords (-t):
 AlphaHelix, LeftHelix, 310Helix, PiHelix, Beta, BetaAnti, BetaPar.
 or
 TOR=VALUE TOR=VALUE ...
 where TOR is the torsion name (Phi, Psi, Omega) and VALUE is the
 torsion value in degree.

Peptide capping keywords (-z):
 NTERM: NONE, H3N+, HCONH, H3CCONH
 CTERM: NONE, O-, OH, OCH3, OC2H5

All parameters are optional with the exception of the input file name (INPUT).

3.1 INPUT ...

This option allows to specify the input file names. VEGA recognizes automatically the format of input files and  the list of supported input formats is shown running VEGA without arguments.
You can load more than one file at once with the same or different file formats to create molecular assemblies. The calculation of connectivity is performed separately for each file to prevent connectivity errors when the molecules are overlapped.
The Data Decompressor Engine allows to manage compressed files as normal unpacked files without any external data decompressor. VEGA supports the following compression formats:

VEGA can recognize .url files and open URLs specified as file names, downloading the molecules for you.

3.2 -0

With this option, VEGA ignores the locale settings and writes always a dot (.) as decimal separator.

3.3 -a[RESNUM]

This option renumbers all residues starting from [RES_NUM]. If this value is not specified, VEGA starts from one. The residue renumbering is very useful when you create an assembly starting from two or more molecules.

3.4 -b

This switch saves molecules without connectivity records when the output format can store this kind of information (e.g. PDB, PDBF, IFF). Many molecular packages interpret incorrectly the CONECT field in PDB files, therefore, to solve this problem, you can save the molecule without connectivity.

3.5 -c[TEMPLATE]

Currently, VEGA supports formal charges (formal keyword), atomic charges based on a fragment database (charmm22_char, charmm36_char, opls_char keywords) and atomic charges based on the Gasteiger-Marsili method (gasteiger keyword) . The Gasteiger-Marsili approach is based on a multi-step procedure:

• Attribution of atom types (by UNIV template).
• Search for explicit charges (e.g. -COO^-, -NH₃⁺, etc).
• Attribution of partial charges through a template (see Appendix A).
• Smoothing of charges.

The formal charges are correctly assigned only if all bonds have the right order (single, double and triple).

3.6 -d[DIELECTRIC]

Use this option If you want to calculate the interaction energy (see -f[FORMAT] option) changing  the default dielectric constant (1.0). Please note that the default value of dielectric constant is stored in the prefs file.

3.7 -e[MOLNUM]

This is a compulsory parameter for the interaction energy evaluation (docking score evaluation, see -f[FORMAT] option). It is required to know which molecule (ligand) is considered to evaluate the interaction energy. You can specify 0 as molecule number to indicate the last molecule in the assembly.

WARNING:
the IFF/RIFF file format is the only one that is able to contain the molecule number information. For this reason, it's impossible to select the ligand by molecule number if you use assemblies (files containing more than one molecule) in other formats. To skip the problem, you can build the assembly on-the-fly specifying the ligand and the receptor as in the following example:

vega receptor.pdb ligand.pdb -f score -c gasteiger -k "CHARMM36 ELECT" -e 0 -o receptor-ligand.xml

Another solution is the use of -y options that enables the detection of molecules:

vega assembly.pdb -f score -c gasteiger -k BRORO -e 2 -o score.xml -y

3.8 -f[OUT.PACK]

With this parameter, you can create an output file in a specific file format. If -f is omitted, the default output format is PDB full standard (see PDB specifications) unpacked. OUT indicates the format and PACK is the optional compression method (bz2, gz, pp and z, see INPUT). This two keywords are case-insensitive.

3.8.1 Calculation formats

3.8.1.1 Information about the molecule

If you want more information about the input molecule, you can use -f INFO option. When you select this operation, VEGA shows many information: total number of atoms, number of heavy atoms, number of residues, number of molecules contained, number of water molecules, molecular weight, coordinates of geometric center, coordinates of mass center, approximative dimensions, total charge (calculated using the atomic charges), dipole, surface area, surface diameter, volume, volume diameter, ovality (only if the probe radius used for surface calculation is null, see -g option), Crippen's logP and lipole, Broto's logP and lipole, Virtual logP (available only in full release), predicted charge (only for proteins, it's calculated searching ionizable groups), aminoacidic charge (only for proteins, it's calculated at physiological pH on the basis of aminoacidic composition), aminoacidic or nucleotidic composition:

************************************
**** Information about molecule ****
************************************

Atoms..............: 48
Heavy atoms........: 25
Residues...........: 1
Molecules..........: 1
Waters.............: 0
Formula............: C19H23NO5
Molecular weight...: 345.384 Daltons
Monoisotopic mass..: 345.157623 Daltons
Geometry center....: 7.1076 3.6789 0.5790
Mass center........: 6.9492 3.5914 0.5256
Appx. dimensions...: 17.4088 10.7721 10.7163
Total charge.......: 0.0003
Dipole.............: 1.0292 Debye
Surf. area (0.00)..: 383.3 Ų (ds=11.0 Å)
Polar area (PSA)...: 50.6 Ų (apolar=332.7 Ų)
Volume.............: 362.3 ų (dv=8.8 Å)
Ovality............: 1.6
logP (Crippen).....: 1.9275
Lipole (Crippen)...: 0.4363
logP (Broto).......: 3.0390
Lipole (Broto).....: 0.4755
Virtual logP.......: 3.1402

Please note that the total number of atoms exceeds the MAXATMINFO key in prefs file, surface area, surface diameter, volume, volume diameter, ovality and logP values are not shown.
If the molecule is a protein or a nucleic acid, the following data are shown:

...

Total charge.......: -23.0004
Predicted charge...: -24
Aminoacidic charge.: -24 

Aminoacidic composition:

Res    N.   N. %     Mass     Mass %
====================================
ALA    46   6.29  3269.690    3.57
ARG    42   5.75  6618.506    7.22
ASN    29   3.97  3309.140    3.61
ASP    43   5.88  4921.520    5.37
CYS    18   2.46  1855.515    2.02
GLU    53   7.25  6789.680    7.41
GLN    46   6.29  5894.132    6.43
GLY    40   5.47  2282.165    2.49
HIS    26   3.56  3565.805    3.89
ILE    37   5.06  4186.861    4.57
LEU    86  11.76  9731.422   10.62
LYS    30   4.10  3875.539    4.23
MET    11   1.50  1443.115    1.57
PHE    25   3.42  3681.328    4.02
PRO    35   4.79  3401.088    3.71
SER    42   5.75  3657.370    3.99
THR    24   3.28  2426.550    2.65
TRP    17   2.33  3165.578    3.45
TYR    35   4.79  5710.992    6.23
VAL    46   6.29  4560.075    4.98

WARNING:
If the protein doesn't have got hydrogens, the predicted charge isn't shown. If protein contains special non-aminoacidic groups and/or metal ions, the predicted charge can be incorrect.

3.8.1.2 Evaluation of interaction energy (molecular docking score)

VEGA can evaluate the ligand-biomacromolecule interaction energy through molecular mechanics calculations. Some scoring functions are implemented (for more details, see -k option).At the present time, only the CVFF force field is implemented. Please remember that ligand and receptor must have correctly assigned charges  (see  -c option) if you want to calculate the electrostatic interaction. You can specify the dielectric constant with -d option (default 1.0) and the ligand (see -e option). After the energy calculation, VEGA shows (or writes in a XML file) the total interaction energy, the components for each atom and residue.

3.8.2 Molecule formats

3.8.3 Plot formats

All these output formats are useful for trajectory analysis (see -m [KEYWORDS] option)

3.8.4 Surface and map formats

VEGA can calculate Van Der Waals and accessible to solvent molecular surface. To enable this function, you have to use the -f[OUTPUT_FORMAT] option as shown in the following table:

The default calculation is the water accessible surface  (1.4 Å sphere radius). To change the solvent radius (probe), you can use the -g[RADIUS] option. If you set the probe radius to null, VEGA calculates the Van Der Waals surface. The standard point density is 10 for one Ų. See -s[POINTS] option to change this value. Click here if you want more information about the surface calculation method.

3.8.5 VRML formats

In order to support the Web publishing, the Virtual Reality Modeling Language (VRML) was implemented in VEGA. To use this function you can use the -f[OUTPUT_FORMAT] option with the following keywords:

The VRML surface formats can also accept the same options of standard surface outputs (see section 3.7.4).

3.8.6 Trajectory formats

VEGA can convert the trajectory files of molecular dynamics simulations to different formats. To enable this function, you have to use the -f[OUTPUT_FORMAT] option as shown in the following table:

3.9 -g[RADIUS]

If you want calculate a surface map with a probe radius different than the default one (the default value is the 1.4Å water radius) without change the prefs file, you can use this option. Please remember that in orded to calculate the Van Der Waals surface, you must set this parameter to zero.

3.10 -i[SHELL RAD SHAPE]

VEGA can solvate a molecule virtually with any type of solvent (e.g. H₂O, CCl₄, etc). The cluster file must be placed in Data/Clusters (Data\Clusters) directory and can be in any VEGA supported format (also packed). This is a solvent assembly with cubic shape (usually with dimension of 50x50x50 Å ), optimized, with uppercase file name without extension (e.g. WATER, CCL4, etc).
SHELL is the solvent cluster name (e.g. WATER). SHAPE is the form of solvatation cluster: BOX for cubic clusters, SPHERE for spherical clusters and LAYER to solvate with a layer of solvent. RAD is a value in Å that followed by BOX, defines the box side, by SPHERE, the sphere radius and by LAYER the layer thickness.

3.11 -j[TORSIONS]

This option define the torsion angles in the molecule. It can be used with the file formats that require the torsions (e.g. AutoDock's PDBQT).

3.12 -k[KEYWORDS]

This option is useful to pass the control keywords when the Info XML (-f NFOXML option) or the Mopac  (-f MOPINT option) or the Score  (-f Score option) format is selected. Remember to use quotas (") if the number of keyword is more than one. In the prefs file, you can specify the default Mopac keywords. The Info XML keywords are summarized in the following table:

All these keywords can be combined separating them by a space character.

The Score keywords that can be used to select one or more score functions, are summarized in the following table:

Keyword	Score function
CHARMM	R6-R12 non-bond interaction evaluated by CHARMM 22 force field provided by Accelrys. To perform this calculation, the parm.prm file must be copied in the ...\VEGA\Data\Parameters directory. This file is not included in the package for copyright reasons.
CHARMM22	R6-R12 non-bond interaction evaluated by CHARMM 22 force field.
CHARMM36	R6-R12 non-bond interaction evaluated by CHARMM 36 force field.
CONTACTS	The scores are evaluated by counting the number of ligand/receptor contacts and by normalizing it by the number of heavy atoms and the mass of the ligand. Moreover, if the receptor is a protein, it generates an interaction fingerprint with a size of 20 bits (one bit for each amino acid type) and a contact map in which the number of contacts per amino acid type is reported. To determine if there is a contact between a pair of atoms, the distance between the two centres is calculated and if it is less than 2.5 Å, then there is a contact. This threshold value can be changed in the prefs file. If -o option is used, the resulting XML file will include the also the two additional scores with extra tag (attributes: id = 1 contacts normalized by the number of heavy atoms; id = 2 contacts normalized by mass), the interaction fingerprint  (fingerprint tag) and the contact map (aamap tag).
CVFF	R6-R12 non-bond interaction evaluated by CVFF force field.
ELECT	Electrostatic interaction. To change the dielectric constant value, use the -d option.
ELECTDD	Distance-dependent electrostatic interaction. To change the dielectric constant value, use the -d option.
MLPINS	Hydrophobic interaction calculated using the Broto's and Moreau's atomic constants*.
MLPINS2	Hydrophobic interaction in which the distance between interacting atom pairs is considered as square value*.
MLPINS3	Hydrophobic interaction in which the distance between interacting atom pairs is considered as cube value*.
MLPINSF	Hydrophobic interaction in which the distance is evaluated by the Fermi's equation*.

All these keywords can be combined separating them by a space character also.

* From Vitoli G. et al., Bioorg. Med. Chem. 18 (2010) 320-19.

"The MLP Interaction Score (MLP_InS) is computed using the atomic fragmental system proposed by Broto and Moreau and a distance function that define how the score decrease with increasing distance between interacting atoms. In detail, the equation to compute such an interaction score is reported below:

where f_a and f_b denote the lipophilicity increments for a pair of atoms and r_ab  is the distance between them. The first sum (p) concerns all ligand’s atoms and the second (m) all enzyme’s atoms. The basic assumption in the calculation of the MLP_InS, which encodes the contributions of the various intermolecular forces measured experimentally in partition coefficients, is that the score is favourable (i.e. negative) when both increments have the same sign (as denoted by the negative sign in in the equation), or unfavorable (repulsive forces) when the score has a positive sign. When the atomic parameters are both positive, MLP_InS encodes hydrophobic interactions and dispersion forces, the importance of which is well recognized in docking simulations, and it accounts for polar interactions, in particular H-bonds and electrostatic forces when the atom ic parameters are both negative".

3.13 -l[MOLTYPE]

This command adds the hydrogens to the loaded molecule/s, saturating all atom valences. MOLTYPE is the molecule type and it can be:

Use the bond order algorithm if the molecule geometry is uncertain (e.g. raw 3D structure or 2D structure), but it works well only if the bond order is correctly assigned.

3.14 -m[KEYWORDS]

This option allows to do measures for each frame or to extract one or more frames of a molecular dynamics trajectory file. You must specify a keyword to set  the kind of measure and optionally  the atom selection:

To select each atom required in the mesure (e.g. A1 A2 etc), you must use  the atom number only, or the following syntax: ATOM:RESNAME:RESNUM. RESNAME and RESNUM are optional if ATOM is univocal. Suppose to have a benzene ring and you would like indicate the third atom, like shown in the following PDB file:

...
ATOM      2  C2  BEN     1       -0.695   1.203  -0.002  1.00  0.00
ATOM      3  C3  BEN     1       -1.389   0.000  -0.006  1.00  0.00
ATOM      4  C4  BEN     1       -0.695  -1.203  -0.007  1.00  0.00
...

you can use, without differences, 3 or C3 or C3:BEN or C3:BEN:1. If you want select the atom 482 in a polypeptidic sequence where only one proline is present, you can indicate it with 482 or CA:PRO or CA:PRO:32, but not CA only:

...
ATOM    481  N   PRO    32      -29.658  -2.153   7.524  1.00  0.00
ATOM    482  CA  PRO    32      -28.294  -1.798   7.139  1.00  0.00
ATOM    483  C   PRO    32      -27.169  -2.471   7.908  1.00  0.00
...
ATOM    495  N   VAL    33      -25.978  -2.393   7.325  1.00  0.00
ATOM    496  CA  VAL    33      -24.749  -2.884   7.927  1.00  0.00
ATOM    497  C   VAL    33      -23.841  -1.699   7.661  1.00  0.00
...

If more than one proline is present in this sequence, you can't use CA:PRO neither.

At the end of the property calculation, VEGA shows the ranges, the average value and the standard deviation. If you want exclude the influence of the water in the calculation of dipolar moment, molecular surface, Virtual logP and molecular volume, you can use the -w option.

3.15 -n

This switch enables the normalization of atomic coordinates. The geometry center of a single molecule or a complex is moved to the origin of Cartesian axes.

3.16 -o[OUTPUT]

With -o parameter, you can specify the name of the output file with or without extension. If the filename doesn't have any extension, VEGA automatically adds the appropriate one on the basis of the selected output format (see -f option). The most common extension used by VEGA are shown in the following table:

Where the column Extension is the file extension, Type is the file type (T = text, B = binary), Add shows if VEGA adds automatically the extension and File Format is the name of file format.
If you execute VEGA without -o parameter, the output is redirected to the console (stdout) or to a special device driver (e.g. PRT: for AmigaDOS). This function is very useful to interface VEGA with another program that can get the input from console. The redirection is possible with text file formats only.

3.17 -p[FORCE_FIELD]

This function allows to assign the atom types using a specified force field template. This is the most complex function implemented in VEGA. The first challenge being the creation of an universal language, called ATDL (Atom Type Description Language) able to describe virtually any atom type. For more information about ATDL, click here. VEGA uses the force field template files stored in Data directory with the extension .tem (lowercase). The name of these files must be uppercase, but the argument of -p option is case-insensitive. In order to assign the correct atom types, VEGA uses a multiple step algorithm:

• Creation of connectivity table.
• Attribution of hybridization of each atom.
• Search for the rings.
• Search for aromatic systems using the Hückel rule.
• Parsing of the selected ATDL template.
• Final attribution of atom types.

Although these steps are very complex, the total process speed is very high.

3.18 -q[METHOD]

Fix the bond order using the specified method that could be: ALL (find the order of all bond) or RINGS (fix the bonds of the aromatic rings making them partial double).

3.19 -r[MODE]

This switch removes the hydrogen atoms: the empty or ALL arguments remove all hydrogens and the APOLAR removes the apolar hydrogens only.

3.20 -s[POINTS]

With this parameter you can change the point density of a surface map. POINTS is the number of points per surface unit (Ų). The default value is stored in the prefs file and usually it is set to 10. For more information about surface calculation, please see the -f[FORMAT] option.

3.21 -t[SECSTRUCT]

The -t option allows to change the protein secondary structure. Two operational mode are available: in the former the user assigns Phi, Psi and Omega torsion values by the syntax TORSION_NAME=value (e.g. Phi=-135), in the latter he put secondary structure name as reported in the following table:

Through the keyword PATTERN=, you can set the secondary structure for each residue according the previous table (Code column). If you specify U code, Phi, Psi and Omega are retrieved from the user-defined values set as explained above.

This option can be used to assign the secondary structure when a Fasta file is loading and if it's omitted, the generic beta strand structure is assigned. All sub-parameters are case insensitive.

3.22 -u

This command adds the side chains to a protein. The side chain database is placed in the Data/Fragments directory and it's called Amino acids L.zip. The side chains are added without hydrogens and so, if you need them, you must use the -l option also.

3.23 -v[CPUS]

Set the number of CPUs used in the parallel calculations. The 0 argument means that all installed CPUs are used.

3.24 -w

This switch removes all the water molecules present in an assembly. Please note that VEGA do not find the water molecules by residue names (e.g. HOH, TIP3, etc), but on the basis of connectivity table. This approach is slower but more precise and independent of residue naming.
You can use the -w option in trajectory analysis to neglect the water influence in the evaluation of dipolar moment, molecular surface and Virtual logP.

3.25 -x[MODE (ID)]

It extracts a molecule from the input database that must be in SDF or ZIP format. The arguments of this  options can be:

3.26 -y

Find the molecules in the assembly using the connectivity information. This feature is useful when you need to select the molecule (ligand) in the interaction energy evaluation (see -e and -k options), because all file formats, excluding IFF/RIFF, can't store molecule information (starting and ending atoms) in the atom list.

3.27 -z[NTERM CTERM]

Add the capping to N- and C-term position of a peptide when it is built from its primary sequence while is loaded from a FASTA file.

4. Command line examples

• vega
  show the available options.

• vega my_file.car
  read my_file.car in Biosym format and print the converted file in PDB format with connectivity.

• vega my_file.cssr.gz -f info
  read my_file.cssr.gz,  uncompress it and show the molecular properties.

• vega "http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1QBQ" -o 1QBQ.iff -f iff
  download the molecule from PDB and save it in IFF format.

• vega my_file.car -o new_file -b -n
  read my_file.car, normalize the coordinates and write new_file.pdb in PDB format without connectivity, adding .pdb to the output file name.

• vega my_file.arc -o new_file.car -f biosym -p cvff
  read my_file.arc in Mopac format, assign atom types and write new_file.car in new Biosym format keeping Mopac charges.

• vega file1.pdb file2.dat -o assembly.iff -f iff -w -a
  read file1.pdb and file2.dat creating an assembly, remove all water molecules, renumber the residues and write assembly.iff in Interchange File Format (IFF).

• vega my_file.mol2 -o new_file -p cvff -c gasteiger -f pdbf
  translate my_file.mol2 from Tripos Mol2 to PDB Fat format creating new_file.pdb. The atom types are assigned, using the CVFF force field and the atomic charges, using the Gasteiger method.

• vega receptor.car ligand.car -f score -k "BROTO CHARMM36" -d 30 -e 0
  calculate the BROTO and CHARMM36 interaction energies between receptor.car and ligand.car with 30 for dielectric constant and shows the results in console. 0 indicates the last molecule in the assembly (ligand.car)

• vega my_file.msf -o surface.srf -f QuantaSrf -s 20
  calculate the surface accessible to solvent (SAS) using the default probe radius and 20 as point density and save it in surface.srf binary file compatible with Quanta package.

• vega my_file.msf -o surface -f BiosymSrf -g 0
  calculate the Van Der Waals surface using default point density and save it in surface.srf ASCII file compatible with Insight II package.
  

• vega my_trajectory.CRD -o my_mesure.csv -f csv -m distance CA:ALA:1 360
  analyze a CHARMm trajectory file measuring the distance between two atoms and storing all data in the my_measure.csv file.

• vega my_file.hin -o solvated.pdb -i water 10 sphere
  solvate my_file.hin with a spherical water cluster of 10 Å radius.

• vega my_file.fas -o my_file_3d.iff -f Iff -t AlphaHelix
  load my_file.fas, assign secondary structure as alpha helix and save it in IFF format.

• vega my_file.pdb -o my_file_3d -t phi=-135 psi=135
  load my_file.pdb, change the secondary structure and save it in PDB format, adding the .pdb file extension.

• vega my_file.pdb -o my_file -f PDBQT -c Gasteiger -p AutoDock -r Apolar -j Flex
  load my_file.pdb, assign the Gasteiger-Marsili atom charges, assign the AutoDock atom types, remove the apolar hydrogens, find the flexible torsion angles and save the molecule in PDBQT format.

• vega complex.pdb -o score.xml -f Score -c Gasteiger -e 2 -k "BROTO ELECT" -y
  load assembly.pdb, assign the Gasteiger-Marsili atom charges, find the molecules, calculate the BROTO (hydrophilic interaction) and ELECT (electrostatic interaction) scores, considering as ligand the second molecule in the assembly and finally save the results in XML format.

5 Default settings (prefs file)

VEGA (command line) starts reading the preference file in order to set the default parameters. This file is placed in Data directory, it's named prefs  and it's in ASCII format editable as a normal text file. Each entry has a keyword with one or more parameters. A semicolon (;) placed in the first column indicates that the line is a remark. Please remember that VEGA doesn't print any warning about incorrect parameters or syntax errors in the prefs file. VEGA ZZ doesn't use this method to set the default parameters. In the following table are shown all available keywords:

For more information about prefs file, see the APPENDIX B.

15. The HyperDrive technology

HyperDrive is a core library including several time-critical functions required by VEGA ZZ for high speed computing. The highly optimized and and parallel code, especially designed for the modern CPUs, allows to speed-up the programs and make faster the development without deep skills in programming. Moreover, the library offers features that are useful not only in developing of molecular modelling software, but also of generic application. In particular, the key features are here summarized:

• Hardware independent.
  You can develop the same application for Linux (ARM, x86 and x64) and Windows (x86 and x64) without changes in the source code.

• Same software for single or multiprocessor systems.
  The library checks the number of CPUs and automatically switches itself from sequential to parallel mode.

• OpenCL support
  Some routines (such as virtual LogP calculation) are written to run on the GPU thanks to OpenCL abstraction layer.

• Simultaneous multithreading (SMT) ready
  It uses the full power of modern multiscalar CPUs with hardware multithreading such as Intel i5, i6, i9 and AMD Ryzen 5, 7, Threadripper.

• Multi core CPU ready
  The latest multi core CPUs provided by AMD and Intel are detected and the parallel execution is automatically enabled.

• SIMD optimization
  The functions that are more frequently called, are written in assembly and optimized by using SSE SIMD instruction set.

• No special compiler required.
  You can use your preferred C/C++ compiler. C++ envelops are included in the headers.

HyperDrive requires an initialization phase that is executed by the host application when it starts. The host application can choose the appropriate HyperDrive version for the installed microprocessor and the HyperDrive detects the number of CPUs switching itself to run in sequential mode (one CPU) or in parallel mode:

After the initialization phase, the host application can call the HyperDrive functions in transparent mode as a normal library: the HyperDrive library select internally the most appropriate code for that hardware/software system and if it can run more than one thread at the same time at hardware level such as for multicore or SMT CPUs, the code is executed in parallel:

HyperDrive library includes several functions that are shown in the following table according to their application field:

17. Creating a new template

VEGA and VEGA ZZ uses two types of template files: the former is for atom types, and the latter is for atomic charges.

17.1 Force field template

By ATDL (Atom Type Description Language), you can expand VEGA adding new atom types and/or new force field templates. Actually, VEGA supports the following pre-defined templates:

A force field template is a file storing the atom type descriptions with uppercase name (corresponding to the force field name) and .tem lowercase extension (e.g. AMBER.tem, CVFF.tem, etc). All template files are placed in Data directory. Please remember that the .tem extension is for all VEGA templates and not for force field only.

In all template files the first column can contain special control characters:

The first line must contain a keyword needed for file type recognition. For force field it must be:

#TemplateFF   [TEMPLATE_NAME]   [VERSION]

where TEMPLATE_NAME is the name of the force field template and VERSION is the revision number.

#TemplateFF CVFF 3.0

After this keyword, you can place the atom type description. The first column is the atom type name (max 8 characters), the second is the atom description in ATDL and the third contains the description of bonded atoms (also in ATDL).
In this last column, each group of atoms limited by parenthesis contains all atoms bonded to precedent atom:

C-300 (O-100 O-100)

This line describes a carboxylic carbon: a sp² carbon bonded to two oxygens making one bond only. More than one levels of parenthesis can be used for complex description of atom types:

C-300 (O-100 O-200 (C-900) C-900)

This line describes a carbonylic carbon of an ester group, bonded to a generic carbon. The O-200 is also bonded to a generic carbon.
Please remember that VEGA reads the line from left to right and thus the more restrictive atom description must placed in more left side of line:

C-400 (C-300 X-900 X-900 X-900)

and not:

C-400 (X-900 X-900 C-300 X-900)

If VEGA finds a C-300 as first or second atom bonded to a sp³ carbon, this is recognized as a more generic X-900 atom and can't be reassigned to the next more specific description.
The description sequence of each atom type goes from more to less specific, from upper to lower line:

cn	C-400 (N-300 X-900 X-900 X-900) ; more specific
c 	C-400 (X-900 X-900 X-900 X-900) ; less specific

If the order of this two lines is swapped, when VEGA finds a carbon bonded to a sp³ nitrogen, the atom type recognized is a generic c an not a cn.

17.1.1 ATDL atom description

Each atom can be defined by a five character string. The first two characters are the element symbol of atom. If the element symbol is one character only, the second character must be a dash (-). For a better description, special elements can be used:

The third character is the bond order: use values from 1 to 6 for real bond order, 0 for non-bonded atom and 9 for a bonded atom with a non-specified bond order.
The fourth character is the ring indicator: use values from 3 to 7 if the atom is a 3 to 7-ring member, 0 for a non-ring member atom and 9 for a non-specified ring atom.
The fifth character is the aromatic indicator: 0 for non-aromatic atom and 1 for aromatic atom.
The ATDL language allows to use AND, OR and NOT operators (&, | and !) inside a logical expression included between square.

Examples:

• C-300
  Generic sp² aliphatic carbon.

• Si900
  Generic silicon with any bond order.

• C-361
  Aromatic carbon, included in a six member ring.

• [C- | N-]900
  the element can be carbon or nitrogen.

• [X- & !Cl]900
  all elements excluding chlorine.

• C-[4 | 3]00
  sp³ or sp² carbon.

• C-4[9 & 9]0
  sp³ carbon in a double condensed ring.

• C-3[6 | 5][!1]
  sp² carbon in 5 or 6 member non aromatic ring.

17.2 Atomic charge template

This template file is much different from the first one, because the atom recognition is based on the residue names and the atom names. The control characters are the same of the force field template.

The first line must contain a keyword needed for file type recognition. For force field it must be:

#TemplateCharge [TYPE] [TEMPLATE_NAME]

where TYPE is the template charge type (Gasteiger or Fragments) and TEMPLATE_NAME is the name of the template. Please remember that the template name must be the same one of the file without the extension.
Example:

#TemplateCharge   Fragments   CHARMM22_CHAR

After this keyword it could be present the optional template title/description:

#Title   [TEMPLATE_TITLE]

Spaces and special characters are allowed.
Example:

#Title   Gasteiger-Marsili charges

After these two keywords, the file can be different if the template type is Gasteiger or Fragments

17.2.1 Gasteiger template

The Gasteiger template is very easy: after the header it's a list of records one for each line. Each record has six fields as reported in the following table:

17.2.2 Fragment template

The fragment template is a little bit complex because it uses some keywords. To define a new residue, you must use the #ResName tag:

#ResName   [NAME1]   [NAME2] ... [NAME16]

e.g.   #ResName   ALA   ALAN

In this way, you define a new residue that it could have one of the specified names. The maximum number of names is 16 and the maximum length of each name is 4 characters.

This tag could be followed by other optional keywords:

#Id   [ID]

e.g.   #Id   AA_ALA

This command defines an unique residue identificator. It can be used by the #Call command (see below) and its maximum length is 31 characters.

#Description   [SHORT_DESCRIPTION]

e.g.   #Description   Alanine (protonated N-terminus)

It allows to specify a short description for the residue or for the macro (see below). Its maximum size is 127 characters.

#Charge   [CHARGE]

e.g.   #Charge   1.0

This optional keyword specifies the residue total charge. The number should be a positive or a negative floating point number.

After these optional keywords, that must be after the #ResName tag, the atom section begins. Each atom is defined in a line with the following fields:

[CHARGE]   [GROUPID]   [BONDS]   [NAME1]   [NAME2] ... [NAME8]

Where:

e.g.   0.3100   1   1   HN   H   H1

This is a complete residue template example:

#ResName ALA
#Id ALA
#Description Alanine
#Charge  0.0000
 -0.4700   1 3 N
  0.3100   1 1 HN   H    H1
  0.0700   1 4 CA
  0.0900   1 1 HA
 -0.2700   2 4 CB
  0.0900   2 1 HB1
  0.0900   2 1 HB2
  0.0900   2 1 HB3
  0.5100   3 3 C
 -0.5100   3 1 O

In red are reported the optional keywords.

In order to simplify the template writing and to make more compact the file size, it's possible to create macros inside the file that must be defined before the use. To begin a new macros, you must use the following command:

#Define   [MACROID]

e.g.   #Define  AMINO_CT

Where the MACROID is the unique identification name of the macro. It have the same function of the #Id command inside the #ResName section. Inside the macro, you can use the #Description, #Call, #Delete commands and the atom records.

#Call   [RESIDUEID_OR_MACROID]

e.g.   #Call   AA_ALA

This command call a residue or a macro executing its commands. It can be placed inside a macro or a residue section.

#Delete   [ATOM_NAME]

e.g.   #Delete   O

This keyword deletes an atom previously defined in a residue section.

Please remember that an atom record inside a macro could replace a previous one if they have the same first atom name. This is a macro example:

#Define AMINO_CT
#Description C-terminus
  0.3400   9 3 C
 -0.6700   9 1 OT1  OCT1 O1   O
 -0.6700   9 1 OT2  OCT2 O2   OXT
#Delete O

Using this macro and an aminoacid residue definition, it's possible to obtain a new one specific for the C-terminal aminoacid:

#ResName ALA ALAC
#Id ALAC
#Description Alanine (negative C-terminal)
#Charge -1.0000
#Call ALA
#Call AMINO_CT

The first call copies the atom definitions from the ALA residue and the second call applies the AMINO_CT macro that change the C atom, add the two carboxyl oxygen, and delete the carbonyl oxygen (O).

19. How-to guide

This section includes some tricks to solve common problems by VEGA ZZ.

19.1 MEP calculation with semi-empirical charges
19.2 Volume calculation
19.3 Trajectory format conversion
19.4 Join two or more trajectory files
19.5 Remove the waters in trajectory files
19.6 Add the side chains to a homology-modelled protein
19.7 AMMP energy minimization
19.8 Installation of Accelrys CHARMM force field
19.9 Conversion of a database to another format
 

19.1 MEP calculation with semi-empirical charges

1. Open the molecule (File Open).
2. Perform a single point Mopac calculation (Calculate Mopac): choose the calculation mode (AM1, MINDO/3, NMDO, PM3), check the total charge, check 1SCF and click Run button.
3. Open the Surface calculation dialog box (Calculate Surface).
4. Select MEP in Type field.
5. Choose the surface type (Dots, Mesh, Solid).
6. Go to Gradient tab, click the rainbow by the right mouse button and select Preset MEP MLP.
7. Return to New tab, check Color by gradient and click Calculate button.
8. Remember that the best way to save the molecule with its surfaces is the use of the IFF file format.

19.2 Volume calculation

1. Open the molecule (File Open).
2. In main menu, select View Information.
3. Press Calculate button and ignore the possible warning messages about the logP calculation.
4. Find the volume value in the output box.

19.3 Trajectory format conversion

1. Open the trajectory file (File Open). If the file name of the associated molecule doesn't have the same prefix  (e.g. mymolecule.pdb and mydynamics.dcd instead of mydinamics.pdb and mydynamics.dcd), you must open the trajectory in two steps: 1) open the molecule (File Open); 2) Open the trajectory file (Calculate Analysis and thus click the open button in the dialog window).
2. Save the trajectory (File Save trajectory), choosing the file format that you need.
3. If you want to save more disk space, you could choose Gromacs XTC as trajectory format, because it uses the XDRF compression algorithm for the floating point data.

19.4 Join two or more trajectory files

1. Make a copy of the first trajectory file.
2. Open the second trajectory file (File Open). If the file name of the associated molecule doesn't have the same prefix  (e.g. mymolecule.pdb and mydynamics.dcd instead of mydinamics.pdb and mydynamics.dcd), you must open the trajectory in two steps: 1) open the molecule (File Open); 2) Open the trajectory file (Calculate Analysis and thus click the open button in the dialog window).
3. Save the trajectory (File Save trajectory), using format, path and file name of the first trajectory file. A requester will be shown: click Append. The trajectory will be joined to the end of the first one.
4. Repeat the operation for each trajectory that you want join.

19.5 Remove the waters in trajectory files

1. Open the trajectory file (File Open). If the file name of the associated molecule doesn't have the same prefix  (e.g. mymolecule.pdb and mydynamics.dcd instead of mydinamics.pdb and mydynamics.dcd), you must open the trajectory in two steps: 1) open the molecule (File Open); 2) Open the trajectory file (Calculate Analysis and thus click the open button in the dialog window).
2. Select the whole molecule without waters (Select No water).
3. Save the new trajectory (File Save trajectory) checking Active only in the Options box.
4. To open the new trajectory, you need an appropriate coordinate file without water molecules. To make it, remove the invisible atoms (Edit Remove Invisible atoms) and save the molecule with the same name of the new trajectory file (File Save As...).

19.6 Add the side chains to a homology-modelled protein

1. Open the backbone file obtained by homology modelling (File Open).
2. Add the side chains (Edit Add Side chains).
3. Check the ring intersections (Calculate Protein check Ring inter.).
4. If one or more ring intersections are found, you must fix them, rotating the Chi1 torsion (Edit Change Angle/torsion). At the end, repeat the ring intersection check.
5. Add the hydrogens (Edit Add Hydrogens), selecting Protein as Molecule type, Residue end as Position of hydrogens and checking Use IUPAC atom nomenclature.
6. Fix the atom types and the charges (Calculate Charges & pot.). Check if the total charge is correct.
7. Save the molecule (File Save As ...). IFF file format is strongly recommended.

19.7 AMMP energy minimization

1. Open the molecule to minimize (File Open).
2. Check the bond types. If they aren't correctly assigned, change them using Edit Change Bonds Find the bond types and finally click Apply. It's also possible to change manually the bonds by Change bonds dialog (Edit Change Bonds) or by context menu.
3. Assign the atom charges (Calculate Charge & Pot.). If you want, it's possible to assign the SP4 potential in order to check if all atoms are correctly recognized. This step is optional, because AMMP fixes automatically the potential if it's not already assigned.
4. Open the AMMP dialog window (Calculate Ammp), select the minimization algorithm (e.g. conjugate gradients), the minimization steps (e.g. 3000), the toler value (e.g. 0.01), the number of steepest descent steps (e.g. 0).
5. Click the Run button.

19.8 Installation of Accelrys CHARMM force field

The Accelrys CHARMM 22 force field allows to do MM/MD calculations of both small and big molecules with less problems than the standard CHARMM force field, because it was expanded with more atom types. For obvious copyright reasons, the ATDL template only (CHARMM.tem) is included in the VEGA ZZ package and not the parameter file (parm.prm), but if you have got an Accelrys software that includes the CHARMm license, you can use it, following this installation procedure:

1. Copy the parm.prm file to ...\VEGA ZZ\Data\Parameters directory.
2. To use it in a NAMD or AMMP calculation, when you fix the potentials (Calculate Charge & Pot.), select CHARMM (not CHARMM22_LIG, CHARMM22_LIPID, CHARMM22_NA and CHARMM22_PROT).

19.9 Conversion of a database to another format

If you want to convert a database to another format, you need to create a new empty database in the desired format:

1. Select File Database Open in the main menu.
2. Choose the destination directory in which the new database will be created.
3. Type the database name in the File name field.
4. In the New database box, select the desired format.
5. Click Create. The new database will be created in the specified directory.
6. Finally click the database name in the file list and press the Open button. The Database explorer window will be shown.
7. Open the database to convert (use Open button in Database box).
8. In Database box, drag & drop the opened database to the empty database. All molecules will be copied from the old database to the new one. If you want stop the copy, click Abort button close to the progress bar of the main window.

20. Frequently Asked Questions

20.1 Generic FAQ

• How is it possible to open a NAMD .coor file including atom properties ?
  The NAMD .coor file format includes only the atom coordinates. VEGA ZZ can open it but the main data of the molecule (atoms, residues, etc) are missing. To avoid this problem, you can open the file from which the .coor file was generated (usually a PDB file), thus merge the atom coordinates of .coor file by selecting File Merge in the main menu. For more information about the merge function, click here.
   

• Converting PDB into mol2 file the atom types and the bond orders are incorrect. Why ?
  If the PDB file doesn't have the hydrogens, VEGA can't detect the correct atom hybridization and the Tripos force field is assigned in wrong way.  This is not a bug and the only way to fix this problem is to add the hydrogens before the conversion.
   

• When I open some PDB files, the connectivity appears incomplete. Why ?
  Starting from VEGA 1.5.0 the PDB CONECT records are read and the connectivity isn't recalculated if the number of that record is more or equal to the number of atoms. To solve this problem, you should recalculate the connectivity for all or for the incomplete atoms, selecting Edit Add Bond from the main menu.
   

• When I try to run VEGA on my Linux RedHat 9 workstation, the message "./vega: relocation error: /usr/local/vega/liblocale.so: symbol errno, version GLIBC_2.0 not defined in file libc.so.6 with link time reference" is shown and the program doesn't start. Why ?
  This error is due to the introduction of the Native Posix Thread Library (NPTL) in Red Hat Linux 9.0. Applications complied with older Red Had distributions (e.g. VEGA and ESCHER NG) are known to experience problems with this library. To work around this problem, you can use the old Linux threads implementation by setting the environmental variable LD_ASSUME_KERNEL. Set it to either 2.2.5 or 2.4.1.
  If you are using c shell, you can enter one of the following at the LINUX prompt:
  
  setenv LD_ASSUME_KERNEL 2.4.1
  
  or
  
  setenv LD_ASSUME_KERNEL 2.2.5
  
  If you are using bash shell, you can enter one of the following at the LINUX prompt:
  
  export LD_ASSUME_KERNEL=2.4.1
  
  or
  
  export LD_ASSUME_KERNEL=2.2.5
  
  Note:
  This problem was eliminated starting from the 1.5.7 Linux release.
   

• How many atoms can manage VEGA and VEGA ZZ ?
  In theory, the maximum number of atoms manageable by VEGA is 2^32 = 4.294.967.296. VEGA ZZ can manage this number of atoms for each workspace and the maximum number of workspaces is 4.294.967.296. These numbers can't be reached by the 32 bit CPUs because their address space is 32 bit wide only.
   

• How many atoms can manage Mopac 7 included in VEGA ZZ package ?
  VEGA ZZ includes two versions of Mopac 7.01-4: Mopac_50_100.exe (max. 50 heavy atoms and max. 100 hydrogens) and Mopac_100_200.exe  (max. 100 heavy atoms and max. 200 hydrogens). The two executables are selected automatically by VEGA ZZ  for a balanced use of the hardware resources. No more than 300 atoms (100 heavy atoms + 200 hydrogens) can be used by VEGA ZZ in Mopac calculations.
   

• Can I use trajectory files and databases with 2 Gb or more sizes ?
  Yes. Starting from VEGA ZZ 2.0.2 and VEGA 1.5.3, the io64 library is linked to the executable allowing to manage files larger than 2 Gb if the file system permit it: FAT12 has a 16 Mb file size limit, FAT16 has a 2 Gb as its limit, FAT32 has 4 Gb as its limit but it's reduced to 2 Gb to allow seek operations. NTFS has a theoretical maximum file size of 16 Exabytes.
  The Linux Ext2 file system has a 4 Tb file size limit and the XFS has a  maximum file size of 16 Exabytes.
  The Amiga Fast File System (FFS) has a 4 Gb file size limit. This limit is braked by the Fast File System 2 with a theoretical maximum file size of 16 Exabytes.
   

• Why are the VEGA ZZ 2.0.6+ IFF files unreadable by previous releases ?
  The 2.0.6 release writes the IFF/RIFF files in the native little endian format (RIFF) by default. The previous releases read the IFF files in big endian format only and so they are unable to understand the RIFF files. This isn't a problem, because you can switch from little to big endian checking Big endian when you save the molecule (File Save as...). Please remember that the 64 bit IFF/RIFF files are unreadable by the previous releases.
   

• Is it available a soft or a PDF manual version ?
  No, the HTML version is available only. If you want, it's possible to build a printable version of the manual, clicking on Printable version in the left summary frame.
   

• Where could I download molecule databases ?
  Some institutions allow to access to their own databases for free. For more information click here.

20.2 VEGA ZZ FAQ

• The IFF files generated by VEGA ZZ 3.0.2+ are shown corrupted by the previous releases. Is it possible to fix the problem ?
  Due to the different visualization method implemented in the newer releases, the IFF files may be shown corrupted by previous releases. To fix the problem, just press the space bar after loading or update your VEGA ZZ installation.
   

• How can I open a trajectory file ?
  Firstly, the trajectory file must be in any format supported by VEGA ZZ (for more information, click here). Some trajectory formats need another file to be opened because they don't contain the information about atoms, residues, etc, but they include the atom coordinates only. The formats requiring an extra molecule file are: AutoDock 4 DLG, BioDock 3.0, DCD, ESCHER NG, GROMACS TRR and XTC and Quanta conformational search .csr.
  VEGA ZZ is able to find automatically the required file starting from the trajectory file name and changing the extension (e.g. my_trajectory.dcd my_trajectory.pdb). It performs changes for three times with three different file extensions (e.g. .iff, .pdb and .crd) that are typical for each trajectory format. If VEGA ZZ can't find the file, it's unable to read the trajectory. To fix the problem, two are the possible solutions:
  - Put in the same directory where is the trajectory, the molecule file with the same file name prefix of the trajectory (see the example above). VEGA ZZ can recognize if that file is compatible with the trajectory and if this condition is not satisfied, an error is shown.
  - Open the molecule file (File Open) that can be in any directory with any name, then open the trajectory file (Calculate Analysis) clicking the open button or dragging the file over the trajectory analysis window.
  For AutoDock 4 DLG, BioDock 3.0 and ESCHER NG, the associated files are obtained from the record inside the trajectory file. The AutoDock 4 DLG loader, if doesn't find  the file, performs the same procedure explained above as last chance.
   

• How is the update procedure ?
  To update the VEGA ZZ already installed in your system, you must uninstall it and thus install the new release in the same directory in which was located the previous one. No new activation is required because the vegazz.lic file isn't removed during the uninstall procedure. Starting from 3.0 release, VEGA ZZ includes an automatic procedure that checks periodically the updates. When they are available, the setups are downloaded from DDL server and installed. The user can perform manually the update selecting Help Check for update menu item.
   

• During the installation, Windows reports this error message: "Error creating registry key and so access is denied". Why ?
  The installer writes in the registry the information to uninstall VEGA. No other data are written.  The error is shown if your user account doesn't have the rights to write the registry. Logon with the administrator account and re-start the installation procedure.
   

• Why doesn't work the REBOL scripts  in my system ?
  With most probability, you installed a software firewall in your PC and so  you must configure it granting the network access to REBOL.exe. The scripting system needs the access to standard TCP/IP communication ports.
    

• Why is the REBOL script execution so slow ?
  The REBOL scripts use the TCP/IP port to communicate with VEGA ZZ. This problem affects Windows 9x and Windows 2000 only. It seems that the TCP/IP management of these OS has an excessive latency. To increase the TCP/IP performances try to use the burst commands that reduces the negotiation time. Windows XP doesn't have this problem and the scripts are executed at full speed.
     

• When I open file and load the DCD file it says "no -m option given", but no pull down menu with -m option is present. Why ?
  You opened a trajectory file directly from the File Open menu item. This procedure is incorrect for the OpenGL operating mode. The correct procedure is the following:
  - Open the whole molecule from File Open menu item.
  - Select Calculate Analysis.
  - Open the trajectory file (click on the button).
  Starting from the 1.4.0 release, you can open the trajectory file from File Open menu item. The associated molecule is loaded automatically without any request.
     

• How can I disable a plug-in ?
  You can disable a plug-in moving it to ...\Plugins\Win32\Store directory.
   

• VEGA ZZ crashes when it's showing complex molecules. How can I solve this trouble ?
  Use the OpenGL Setup utility to change the OpenGL driver from hardware to Microsoft or Mesa 3D .
   

• VEGA ZZ has low 3D performances with Matrox P-Series graphic cards when the FAA-16x anti aliasing or the stereo view is enabled. Why ?
  These graphic cards use the alpha channel to perform the aliasing reduction and the stereo view. So, if you open applications that use the alpha key, the OpenGL performances go down. A common situation is an application that uses the transparencies to make glass windows (e.g. VEGA, Miranda, WinAmp, etc). The solution is to disable the glass windows (see the control panel of the specific application) or to close the program. This problems affects Windows 2000 and not Windows XP.
   

• How can I improve the graphic quality ?
  If you have an ATI, Matrox P-series, NVIDIA graphic card, enable the anti-aliasing in the control panel of the display driver. By default, this setting is disabled. In the OpenGL mode, the Matrox driver supports the 16x anti-aliasing only.
  Enable the vector anti-aliasing in the VEGA ZZ View settings window.
   

• How does VEGA add the solvent molecules ?
  VEGA uses a pre-calculated solvent cluster placed in ...\VEGA ZZ\Data\Clusters directory that is a PDB gzipped file. When you add solvent clusters to a solute, VEGA performs these steps:
  
  - load the solvent cluster;
  - move the solute at the centre of the cluster (it have a cubic shape);
  - cut the volume occupied by the solute removing the bumping molecules;
  - cut the shape as you selected in the graphic interface (box, sphere, layer).
  
  When you choose Sphere, VEGA cuts a sphere of specified radius cantered at the barycentre of the solute. When you select Layer, it cuts the molecules exceeding the distance between them and the closest atom on the surface. Choosing the Box mode, VEGA cuts the solvent molecules outside the box user-defined dimensions. The box is cantered at the barycentre of the solute as for the sphere mode.
  This is a generic method for all kinds of solvents. The direction of the water h-bonds referenced to the solute is not taken in account. For this reason, after the solvation, you must optimize the system performing an energy minimization and, eventually, a short molecular dynamics.

20.3 VEGA ZZ activation problems.

• I didn't received the Activation Key because I inserted a wrong e-mail address in the registration form. How can I change it in order to activate the software ?
  The procedure is very easy:
  - Connect to DDL license server: http://www.ddl.unimi.it/licman/login.htm.
  - Login with the wrong e-mail address and the password specified during the registration procedure.
  - In the menu, select Update user details and click Go !
  - Change the e-mail address and click Update.
  - Repeat the activation procedure with the new e-mail address.
  - A warning message will be shown, informing you that the Product Key is already active.
  - Request a copy of the Activation Key that will be sent to you at the new e-mail address.
   

• My Activation Key is lost. Can I request a copy ?
  Yes ! Repeat the activation procedure: a warning message informs you that your Product Key is already active. Request a copy of it clicking the link.
   

• I have several PCs and I would like to install VEGA ZZ on all of them. Can I obtain more than one Activation Key ?
  Yes ! There are no limits in the number of activations. Please use the same e-mail address for all activations to avoid to compile the registration form each time.
   

• My Activation Key is expired. How can I obtain a new one ?
  Repeat the activation procedure and replace the vegazz.lic file with the new one sent to you by the activation server.
   

• I received the e-mail with the Activation Key but I'm unable to open it. Why ?
  The Activation Key is a encrypted binary file and VEGA ZZ only is capable to decrypt and read it. You must follow the activation procedure reported in the e-mail and in the activation wizard: you must save the vegazz.lic file in the Data folder placed in the installation directory. Starting from the 2.0.8 release, if you try to open the vegazz.lic file, it's automatically copied in the installation directory and if it's already present, a warning message is shown.
   

• When I try to install the Activation Key, the invalid license file name message is shown. How can I fix this problem ?
  With most probability, you changed the the activation file name from vegazz.lic to another one or you tried to open it directly from the e-mail client that decodes it, creating a temporary file that isn't named correctly.
  Try to save the file and double click on it.
  Another common problem is due to Windows default setting, hiding the extension of known files. In particular, if you rename the activation key to vegazz.lic, the OS keeps the previous .lic extension making the real file name as vegazz.lic.lic even if vegazz.lic file name is shown. There are two possible solutions: 1) remove the .lic file extension; 2) go to the file explorer settings (Folder options window -> View tab -> Advanced settings list) and uncheck Hide extensions for known file types.
   

• VEGA ZZ says to me that my system has an invalid host ID or a CRC error is present in my Key. Few days ago, the software worked fine. Why ?
  Your host ID is changed and this is possible when the hardware network configuration is changed adding a new network card, modem, IEEE 1394 card etc or updating the motherboard BIOS and/or device drivers. In this situation, the solution is repeat the activation procedure.
   

• It's possible to create an Activation Key for a computer not connected to Internet ?
  Yes, it's possible following this procedure:
   
  NC is the PC not connected to Internet.
  C is the PC connected to Internet.

1. Download VEGA ZZ with C.
2. Transfer the package from C to NC (e.g. by pen drive, CD, etc).
3. Install the package on NC and start VEGA ZZ. The activation wizard will be show.
4. Annotate the Product Key. Please remember that it's not the same of C.
5. Start Internet Explorer in C and connect to http://www.ddl.unimi.it/licman.
6. Put the Product Key of NC, your e-mail address and complete the activation as usual.
7. When you receive the e-mail with the vegazz.lic file, transfer it to NC and copy it un the ...\VEGA ZZ\Data directory. VEGA ZZ on NC is now operative.

22. Bugs

VEGA ZZ and VEGA are pieces of software with many functions, therefore it might be possible to discover minor bugs. 

22.1 Bug report

VEGA ZZ 3.0 contains a built-in bug report utility called madExcept that help you to send the data needed by us to identify and fix the problem. If a serious error occurs, this dialog window is shown:

in which it's possible to choose different actions:

• continue application: ignore the severe error and continue the VEGA ZZ execution. This choice is not recommended, but it could be useful to save the data before to restart;
• restart application: close the application loosing all data and restart it;
• close application: close the application loosing all data;
• show bug report: show all data to identify the bug (for skilled people only):

 

changing the tabs, its possible to show the data that will be sent to us;

• send bug report: start the wizard to send us the bug report (preferred action):

 

Complete the form typing your name and your e-mail address, check remember me if you want save your contact information and click Continue.

 

 

Explain the situation in which the error occurs and click Continue or Skip if you have nothing to explain.

 

 

Clicking Continue, the report will be sent to us. Please note that no sensitive personal information will be sent to us and all data will be used for debug purpose only.

If you find a non-critical bug not showing the report utility you can contact us by this e-mail address: bugreport@vegazz.net.
For other questions please refer to the Authors address in copyright section. 

22.2 Known bugs

22.2.1 Amiga version

• The powerpacker.library accepts only standard Amiga DOS paths and not Unix-like syntax of ixemul.library. The Data Decompressor  Engine shows an error (file not found) if a file is powerpacked and the path has the Unix-like syntax.

• The HyperDrive library is statically linked and it doesn't support symmetrical multiprocessing and OpenCL.

22.2.2 VEGA ZZ

• Using multi-monitor systems (e.g. dual head graphic cards or two graphic cards) under Windows 9x/ME, the 3D hardware acceleration is not available. This is not a VEGA bug, but a limit of the Microsoft operating system. Windows 2000/XP don't have this problem.

• When the monitor in suspend mode is waked up, the double buffer of the main window could be corrupted. You must force the refresh, minimizing and restoring the main window.

• When you save an image using the hardware rendering and you installed a Matrox P-Series graphic card, the labels aren't rendered. This is a bug in the Matrox OpenGL driver: the switching of the device context is not detected. The rendering with the software driver (provided by Microsoft) works fine.

• The PDF, PostScript, EPS and LaTex drivers don't support transparencies and smoothed vectors.

• See the compatibility list for the graphic accelerators.

23. Development information

The VEGA package was originally developed to run with AmigaOS using its graphic interface. The GUI was totally rewritten to work with all Windows systems and takes the advantages of the OpenGL graphic API.

23.1 Hardware for beta testing

In this section, you can find the hardware platforms used to develop and test VEGA and VEGA ZZ:

• PC IBM compatible: AMD Ryzen 9 3900X 12 core 3.8 GHz, Windows 10 Professional x64, 32 Gb DDR4 Ram, NVIDIA GeForce RTX 2070 Super 8 Gb DDR6 PCIe card, HTC Vive Pro Eye HMD, 512 Gb NVMe SSD, 6.0 Tb 7.200 rpm HD, SATA DVD-Writer, 10/100/1000 Ethernet card.

• Asus RS700-E7/RS8 Intel: 2 Intel Xeon E5-2620 eight core 2.0 GHz, CentOS 6.2/Windows 7 Professional x64, 64 Gb DDR3 Ram, Aspeed AST2300 16MB VRAM, 3x 500 Gb SATA-2 7.200 rpm HDs, DVD-Writer, 4x 10/100/1000 Ethernet cards.

• PC IBM compatible: AMD Phenom II X6 1090T six core 3.2 GHz, Windows 7 Professional x64, 8 Gb DDR3 Ram, Sapphire/ATI HD5770 1 Gb DDR5 PCIe card, 512 Gb SSD SATA-3, 2x500 Gb 7.200 rpm SATA HDs,  SATA BD-Writer, SATA DVD-Writer, 10/100/1000 Ethernet card.

23.2 Development tools

• Amiga systems:
  Gcc 2.7.2 for Amiga, Cygnus Editor Professional V3.5, Enforcer V37, MungWall.
• Linux systems:
  Gcc for Linux, Nedit.
• Silicon Graphics systems:
  IRIX 6.2 development toolkit, Nedit, Rasmol, Cosmo Player.
• Windows 7/810 systems:
  Embarcadero RAD Studio XE 10.2, Microsoft PSDK, MinGW 4.6.3, Inno Setup Compiler.

No endorsement of any hardware of software should be inferred

24. History

• Release ZZ 3.2.3.28 (05/04/2023)
  - DNA/RNA builder tool.
  - Calculation of the contact score with interaction fingerprint generation.
  - Calculation of RMSD without alignment and with/without hydrogens.
  - Calculation of RMSD with symmetry correction and with/without hydrogens.
  - Calculation of amino acid composition when you save in infoxml format.
  - New scripts: DNA tools\DNA to PNA.c (converts DNA to PNA), DNA tools\RNA to DNA.c (converts RNA to DNA.c), Docking\Hypervolume analyzer.c (calculates the shared area and volume of multiple docking poses).
  - New extended commands: BuildDna.
  - Fix: detection of Mopac 7 executables.
  - VEGA command line is now based on the VegaBase library.
  - VEGA command line can list the molecules in a database.
   
• Release ZZ 3.2.2.21 (29/03/2022)
  - Fix: ZINC downloader.
  - Fix: proline protonation state when you add the hydrogens.
   
• Release ZZ 3.2.2.20 (22/03/2022)
  - VEGA breaks the barrier of 64 logical CPUs supporting multiple NUMA nodes and processor groups.
  - Added MetaClass scripts to predict metabolic reactions of a given molecule or of a set of molecules according to MetaQSAR rules.
  - Added -NH2 as C-terminus type of capping when you build a peptide.
  - Added -z option to the command line version to specify the capping of N- and C- terminus residues when you build a peptide.
  - Fix: mol2 loader.
  - New scripts: Docking\GOLD score extractor.c (extract the docking score of each pose from the mol2 file generated by GOLD).
  - Updated gl2ps library to 1.4.2.
  - Updated Opsin to 2.6.0 release.
    
• Release ZZ 3.2.1.33 (01/06/2020)
  - Experimental OpenVR rendering mode for HMD display with head tracking support.
  - Equirectangular 360° images taken with your panoramic camera (e.g. LG 105R, Insta 360, Samsung Gear, etc.) can be used as SkyBoxes. 3D equirectangular pictures (top/bottom) are also supported.
  - Now the color gradients for skyboxes are generated programmatically and the user can create them just editing a csv file.
  - Added number of angles, bonds and atom type occurrences to InfoXML output format.
  - Added the capability to assign formal charges.
  - Added Edit Remove Counterion menu item.
  - Peptide builder: now you can set the secondary structure for each aminoacid and specify the capping for both N- and C-terminus. BuildPept and SecStruct commands were updated to support these new functions.
  - Database Explorer: added two new functions (remove counterions & waters and keep only the largest molecule) when you put molecules into a database.
  - Rescore+ now can calculate also RPScore (only for proteins).
  - Pockets plug-in: added the capability to to rank the pockets by docking score calculated by PLANTS or Vina selecting one or more probe molecules.
  - Fix: access violation ionizing cyclic polyamines.
  - Fix: dialog placement with Windows 10.
  - Fix: drag & drop when you run VEGA ZZ with administrative privileges.
  - New scripts: Build\Peptide library.c (Build a library of peptides from a given peptide length and aminoacid composition), Calculation\EQeq charges\EQeq non-periodic.c, Calculation\EQeq charges\EQeq periodic Ewald.c, Calculation\EQeq charges\EQeq periodic.c (calculate atomic charges by EQeq method).
  - New extended commands: MolDelete, SegDelete.
  - Removed obsolete tools: VEGA SE, VEGA WE, WarpGate, WarpKeyGen and WarpTel.
  - Removed Molinspiration scripts.
  - Removed obsolete scripts: Communication\ActiveSync VRML send.c,  Communication\FTP put.r, IrDa Communication\VRML send.c, Communication\Web server.r
  - Renamed scripts: Automatic model builder.c to Enrichment factor optimizer.c; Enrichment analysis.c to Enrichment factor analysis.c; Model builder.c to Enrichment factor optimizer (manual).c
    
• Release ZZ 3.2.0.9 (04/09/2019)
  - Full screen mode.
  - Side-by-side (SBS), half side-by-side, cross-eye, top and bottom, half top and bottom stereoscopic modes.
  - Rendering of 360° (equirectangular) and cube (cube faces) panoramas.
  - Support for 3Dconnexion devices (e.g. SpaceMouse, SpacePIlot, etc.). At least the 17.5.5 version of is required.
  - VEGA ZZ is now DPI aware and supports high DPI desktops (e.g. 4k).
  - Change: default font is now Segoe UI.
  - Fix: detection of x64 executables for docking.
  - New extended commands: ConRec, ConRecPause, ConRecResume, ConRecStop, RotateView.
  - New system variables: ConRecStatus, IsFullScreen.
    
• Release ZZ 3.1.2.39 (03/05/2019)
  - First full 64 bit release of VEGA ZZ (the 32 bit version is still included in the package).
  - EMPIRE .arc and .dat loader.
  - WarpEngine APBS version 1.0.
  - WarpEngine MOPAC version 2.0.
  - WarpEngine PLANTS version 2.0.
  - WarpEngine RESCORE+ version 1.0.
  - ARFF data export from SQL databases for machine learning programs.
  - Added the capability to save MD movies in AVI XVID, Matroska video H.264, MP4, MPEG-2 transport stream, MPEG-4 AVC, MPEG-H HEVC (h265) and QuickTime formats.
  - Added the possibility to save the scene in STL (ASCII and binary) format for 3D printing.
  - Tree2C stand alone tool (Weka decision tree to code converter).
  - Paste data (from Excel, text, etc.) to a SQL database.
  - Editing of the column/field of a SQL database.
  - Updated "Training and test set creator.c" script in order to generate homogeneous data sets.
  - New extended commands: RemInvAtoms, RemVisAtoms, ResetView, UndoPop.
  - New system variables: Area, Asa, Charge, MassMI, Ovality, Psa, Sas, Sav, Sdiam, Vdiam, Volume.
  - New scripts: Development tools\Decision tree to C converter.c (it converts a Weka decision tree to C code).
  - Fix: removed glitches from VRML and PovRay scenes.
  - Removed OpenGL setup and WireGL.
  - Updated gl2ps library to 1.4.0.
  - Updated Opsin to 2.4.0 release.
  - VEGA WE supports SSL conncetions.
  - Built with RAD Studio 10.2.3 Tokyo.
   
• Release ZZ 3.1.1.42 (06/04/2017)
  - MetaQSAR plug-in: a complete system to manage metabolic reactions.
  - WarpEngine technology for collaborative computing (experimental implementation).
  - Database Explorer now can generate stereoisomers, geometric isomers and tuatomers. It can also adjust the ionization state according to the specified pH.
  - Change the ionization of a molecule according to the pH value.
  - The custom selection tool accepts SMARTS strings.
  - SMARTS atom typing.
  - Calculation of HLB (Davies, Giddin, PSA and mean value).
  - Added the support for MOPAC 2016.
  - PHP 5 scripting engine (included in the package).
  - Python 3 scripting engine (included in the package).
  - Added SSL/TLS secure connections.
  - Solvation code is now parallelized.
  - Fix: now VEGA can detect more than 32 CPUs.
  - Fix: AMD R7 graphic card issue (Z-buffer glitches).
  - Fix: Windows 10 "snap to window" function.
  - VEGA WE includes the Web service to calculate log kw IAM.MG/DD2 for PubChem molecules.
  - New extended commands: DbSqlTableInfo, Ionize, SelSMARTS, SMARTSCount, TrjClustCoord, TrjClustTor, TrjClustTorRmsd and UnSelSMARTS,
  - New system variables: BmLipole, BmLogP, GcLipole, GcLogP, HLBd, HLBg, HLBpsa and MopacExe.
  - New scripts: Ammp\Automatic Boltzmann jump.c (it performs the conformational and cluster analysis of a given molecule), Build\Solvent cluster racemizer.c (it creates a racemic mixture from a solvent cluster), Calculation\Database properties.c (calculate several properties for all molecules included in a database), Calculation\Log kw IAM (calculate log kw IAM.MG/DD2 of a given molecule), Calculation\Molinspiration\Database properties.c (get some properties from Molinspiration server for each molecula included in a database), Calculation\Molinspiration\miLogP.c (get logP from Molinspiration server), Calculation\Molinspiration\TPSA.c (get TPSA from Molinspiration server), Database\ZINC get by ID.c (download a molecule from ZINC database), Docking\Best score of isomers.c (keep the best docking score of each isomer set), Docking\Mean score of multiple poses.c (calculate the mean score of multiple docking poses), Examples\NAMD minimization.c (it shows how to use the NAMD helper to run a simple energy minimization), Docking\PLANTS\RMSD calc.c (calculate the RMSD between the poses of a docking calculation) and QSAR\Virtual screening\CSV to SVM light.c (convert a CSV file to SVM light format).
  - Updated gl2ps library to 1.3.9.
  - Updated Opsin to 2.2.0 release.
  - CCl₄ solvent cluster.
   
• Release ZZ 3.1.0.21 (15/12/2015)
  - Added the possibility to export a database in CSV format.
  - Added the support to manage Microsoft Access 2007 (.accdb) databases.
  - Added the use of atom constraints for Mopac calculations (Mopac2007 or greater is required).
  - Fingerprint search and comparison in Database explorer.
  - Fix: flexible torsion count.
  - Fix: small bug in NAMD calculation.
  - New extended commands: Fingerprint, FpSimilarity, WksCpyAtm, OpenDatatDir.
  - New scripts: Database\Count functional groups.c (count the number of functional groups of each molecule included in a database), Docking\Contact surface.c (measure the ligand (receptor contact surface), Docking\Rescore+,c (evaluate docking poses with different scoring functions), Homology modelling services\FUGUE.htm (easy access to FUGUE server), Homology modelling services\I-TASSER.htm (easy access to I-TASSER server), Homology modelling services\Phyre 2.htm (easy access to Phyre 2 server), Homology modelling services\ROBETTA.htm (easy access to ROBETTA server), Homology modelling services\SWISS-MODEL.htm (easy access to SWISS-MODEL server), QSAR\Data normalizer.c (normalize the column values in 0-1 range), QSAR\Principal component analysys.c (perform the PCA of a given dataset), Trajectory\APBS trajectory.c (calculate the APBS solvation energy for each trajectory frame).
   
• Release ZZ 3.0.5.12 (25/11/2014)
  - Fix: ChemDraw CDX loader when the file includes external connection points.
  - Fix: missing atom charges in .arc file when you run Mopac2012. The PRTCHAR keyword is automatically added when the input file is prepared for Mopac 2012.
   
• Release ZZ 3.0.5.10 (13/11/2014)
  - Fix: access violation when you save ions in X-Plor PSF format.
   
• Release ZZ 3.0.5.9 (4/11/2014)
  - Combinatorial SMILES builder.
  - LiGen grid, pharmacophore and pocket loaders (text and binary formats).
  - Added the support for IUPAC (read only) and SMILES databases (read and write).
  - Fix: small bug when the molecule information is shown.
  - Fix: 2D preview in optical stricture recognition.
  - Visual C++ redistributable package no more needed by Indigo library. 
  - Support for NAMD multicore x64.
  - Updated Opsin to 1.6 release.
   
• Release ZZ 3.0.4.18 (7/07/2014)
  - Support for GRAMM output that can be analyzed as a trajectory.
  - In the systematic conformational search, you can now select the ending angle value for the rotation.
  - Conformational search and Bond/angle/torsion change dialogs can load and save the selections.
  - Conversion of the atom coordinates from any dimension to 2D and 3D, hence AMMP 2D to 3D.c was removed.
  - Added Calculation Docking menu item.
  - Added the possibility to run scripts directly from the main menu just changing the powernet.xml configuration file in Config directory.
  - Fix: missing connectivity when you solvate a molecule.
  - New scripts: Build\Protein mutagenesis.c (build a database of mutants from a given protein), Communication\Download molecule from URL.c (download a molecule from a given URL), Docking\WarpEngine GRAMM extractor.c (extract the complexes from WarpEngine GRAMM output), Docking\RPScore.c (calculate the RPScore of a given protein-protein complex or a trajectory of protein-protein complexes), QSAR\Virtual screening\Enrichment overfit.c (enrichment factor optimization for virtual screening calculations), Trajectory\PELE PDB fix.c (fix the PDB files generated by PELE to be read by VEGA ZZ).
  - Replaced Cano and Dingo libraries by Indigo Toolkit 1.1.12.
  - Updated AMMP to 2.4.1 release.
   
• Release ZZ 3.0.3.18 (24/04/2014)
  - Added the capability to automatically center and zoom the current atom selection.
  - ChemDraw CDX loader.
  - Now the trajectory analysis tool can calculate the ovality.
  - Mopac 2012 x64 is now supported and automatically detected when installed into ...\VEGA ZZ\Bin\Win64 directory.
  - Optical structure recognition: added the capability to open password-protected PDF files.
  - Fix: Gaussian loader when load the output.
  - GriDock: fixed the problem to read mdb databases when the OS is Windows x64.
  - New scripts: Utilities\Bin2h.c (convert a binary file to a C header), Utilities\CPU load.c (show the CPU load).
  - Updated mupdf to 2.4 release.
  - Updated Opsin to 1.5.0 release.
  - Updated Tcc to 0.9.26 release.
  
  Warning: due to the different visualization method implemented in this release, IFF files may be shown corrupted by previous releases. To fix the problem, just press the space bar after loading.
    
• Release ZZ 3.0.2.48 (11/11/2013)
  - Build 3D molecules by IUPAC name (powered by OPSIN).
  - Merck MMD database management (read only).
  - Spillo RBS saver.
  - SketchEl editor was replaced by Ketcher, because it have some problems with the latest JVMs.
  - Added the capability to download and open molecules by URL (both ZZ and command line versions).
  - Added the capability to open more than one molecule when you analyze a trajectory.
  - Now you can copy & paste URL and VEGA download the molecule for you.
  - Fix: access violation when VEGA ZZ is closed.
  - New system variable: TorRealMolAct.
  - New extended commands: DbGetMolName, DbSetMolName, DbSortMolNames, DbSqlExec.
  - New scripts: Calculation\APBS membrane energy.c (Evaluate the energy required by a molecule to leave the hydration shell and to reach a biological membrane), Calculation\APBS solvation energy.c (Evaluate the solvation energy), PubChem\Database rename\By CID.c (rename all molecules in a database by CID), PubChem\Database rename\By IUPAC.c (rename all molecules in a database by IUPAC), PubChem\Database rename\By name.c (rename all molecules in a database by the most common PubChem name), PubChem\Download\Multiple by CID.c (get multiple 3D structures from PubChem by specifying their CIDs), PubChem\Download\Multiple by name.c (get multiple 3D structures from PubChem by specifying their names), PubChem\Download\Single by CID.c (get a molecule from PubChem specifying its CID), PubChem\Download\Single by name.c (get a molecule from PubChem specifying its name), PubChem\Get\CID.c (obtain the CID code of the current molecule from PubChem), PubChem\Get\IUPAC name.c (obtain the IUPAC name of the current molecule from PubChem), PubChem\Get\Multiple IUPAC names.c (obtain the IUPAC names of some molecules by specifying their CID), PubChem\Get\Name.c (obtain the name of the current molecule from PubChem), PubChem\Get\XLogP.c (get the XLogP value of the current molecule from PubChem), QSAR\Enrichment analysis.c (analyze the enrichment factors in order to perform a virtual screening setup), QSAR\Model validator.c (validate a QSAR model).
  - The command line version now can convert the trajectories to different formats.
  - WakeUp, WakeUpServer and WakeUpService tools are now included in the package. They allow the remote PCs to be turned on by Wake On Lan standard even if you aren't in the local network.
  - Increased SSE support in HyperDrive library with significant performance improvements.
   
• Release ZZ 3.0.1.22 (18/2/2013)
  - New script: Database\Merge Mol2.c, Database\Merge SDF.c, Database\Splitter.c, Docking\Rescore database.c, Examples\Mini-XML demo.c.
  - GraphApp library is now replaced by GraphAppZ for a better integration in VEGA ZZ environment.
  - Fix: av.dll problem when you save a trajectory in MPEG 1/2 format.
  - Fix: division by zero error scrolling the manual pages.
  - New extended command: TurboEx.
  - Updated gl2ps library to 1.3.8.
   
• Release ZZ 3.0.1.10 (15/11/2012)
  - Mol2 database management.
  - New ATDL routines for version 4 templates. The old templates continue to use the previous routines.
  - Added the support for Mopac 2012.
  - New scripts: Database\Force field check.c, Docking\APBS binding energy.c, Docking\PLANTS\Receptor.c, Docking\PLANTS\Patch bin 1.1.c.
  - Updated  Docking\PLANTS\Docking.c script to manage the side chain flexibility.
  - Fix: access violation when you close a single database.
  - Fix: copy to clipboard of AMMP\Interaction energy.c script.
  - Fix: SQL queries.
  - Fix: trajectory file lock when the molecule is closed.
  - Fix: dialog update adding hydrogens and ions.
  - Fix: PSA calculation of a selected set of atoms.
  - New system variable: Mol.
  - New extended commands: DbReOpen, DbUpdate.
   
• Release ZZ 3.0.0.52 (18/7/2012)
  - New script: Docking\PLANTS\Docking.c
  - Fix: random access violation closing GraphApp scripts.
   
• Release ZZ 3.0.0.51 (10/7/2012)
  - VEGA command line now includes ARM Linux executables for Raspberry PI (ARM1176JZF-S & VFP optimized).
  - Fix: menu activation when you update a molecule in the database.
  - Fix: SQL database engine and fast index creation.
  - Fix: SDF database engine reading molecule names.
   
• Release ZZ 3.0.0.49 (28/6/2012)
  - Fix: QSAR\Automatic linear regression.c.
  - New scripts: QSAR\Table join.c, QSAR\Training and test set creator.c.
   
• Release ZZ 3.0.0.48 (21/6/2012)
  - Saver, DB engine, copy special, and InfoXML format updated to support  InChIKey.
  - DB engine updated to support ODBC and Microsoft Access databases.
  - Copy to clipboard 2D sketches (copy special).
  - New popup menu sensible to the context.
  - Save the picture of 2D sketches.
  - 2D preview in SMILES editor and database explorer.
  - Optical structure recognition (provided by OSRA).
  - Customizable database reports.
  - Editing of database fields.
  - PSA with color smoothing (OpenCL powered).
  - Color by flexible torsion (normal and AutoDock).
  - Automatic shutdown at the end of the calculation.
  - New graphic interface with magnetic windows.
  - Possibility to click on windows entirely covered by other ones.
  - User-defined window layouts.
  - Ethanol cluster for solute solvation.
  - AutoDock Vina is now included in the package and it's fully supported.
  - Automatic update check and setup.
  - REBOL installation no more required.
  - Fix: Mopac .arc file recognition.
  - Fix: SQLite update procedure.
  - Fix: PSA calculation.
  - New system variables: ConfigDir, ConLines, InChIKey, IsWOW64, MassAct, ScriptsDir, WksLocked.
  - New extended commands: BuildPept, ConGetLine, DbLock, OpenEx, SaveImg2D, SecStruct, SetLastFileName, Smiles.
  - New scripts:

- Calculation\XLOGP2.

calculate the logP by XLOGP V2 method.

 

- Database\SMILES to database.c

convert a file containing SMILES strings to a database.

 

- Docking\PLANTS\Rescore ChemPlp.c
- Docking\PLANTS\Rescore Plp.c

- Docking\PLANTS\Rescore Plp95.c

evaluate ligand - receptor interactions by different PLANTS scoring functions.

 

- Docking\Vina\Docking.c

Vina graphic interface.

 

- Docking\Vina\Ligand.c

prepare the ligand to be docked by Vina.

 

- Docking\Vina\Receptor.c

prepare the receptor to be docked by Vina.

 

- Docking\Vina\Virtual screening.c

complete easy-to-use virtual screening system based on Vina.

 

- Docking\X-Score.c

evaluate ligand - receptor interactions by X-Score.

 

- Interaction surface\CHARMM interaction surface.c

show the ligand-receptor interaction surface using the CHARMM force field.

 

- Interaction surface\Lipophilic interaction surface.c

show the ligand-receptor lipophilic interaction surface.

 

- Interaction surface\MEP interaction surface.c

show the ligand-receptor electrostatic interaction surface).

 

- Interaction surface\MLPInS color ramp.c

normalize the color ramp of surfaces calculated by MLPInS interaction surfaces.c

 

- Interaction surface\MLPInS interaction surfaces.c

show the ligand-receptor MLP_InS interaction surface

 

- Movie\Sec. structure anim.c

create a movie changing the secondary structure.

 

- QSAR\Automatic linear regression.c

generate all possible regression models.

 

- QSAR\Linear regression.c

perform multiple linear regressions.

 

- Trajectory\DCD fix for VMD.c

patch buggy DCD files generated by pre-3.0.0 VEGA ZZ releases.

- New batch files: Namd.cmd (NAMD command line interface), NamdClean.cmd (clean the directory removing useless files and keeping NAMD results), NamdMulti.cmd (perform multiple NAMD calculations considering all input files in a given directory).
- AutoDock 4 and AutoGrid 4 were compiled by gcc 4.6.3 for x86 and x64 Windows with a significant performance improvement (from 2 to 3 time faster than the previous build made by gcc 3.4.5).
- AutoDock Vina 32 and 64 bit version built by gcc 4.6.3 are now included in the package. Vina 64 bit is up to two time faster than the original 32 bit version.
- gcc and gfortran 4.6.3 were used to update both 32 and 64 bit executables (AMMP, ChemSol2, ESCHER NG, Fpocket, HyperDrive, InChI, Mopac7, Predator, PropKa, VEGA command line).
- Updated gl2ps library to 1.3.6.
- Updated InChI library to 1.03.
- Updated REBOL to 2.7.8.
- VEGA ZZ in now compiled by RAD Studio XE.
- Support of Wine emulation layer discontinued.
- VEGA command line for Linux includes binaries for both x86 (32 bit) and x64 (64 bit) operating systems in a unique package. Now, the same package contains also: AMMP, ESCHER NG, GriDock, Mopac 7 and SQLite.
 

• Release ZZ 2.4.0 (4/10/2010)
  - OpenCL acceleration for surface and Virtual logP calculations. The OpenCL support is available for all VEGA releases (ZZ for Windows x86, command line for Windows x86, x64 and Linux x86, x64).
  - SMILES loader, saver and editor.
  - Bond length check.
  - New interaction analysis tool.
  - MassTools: mass spectrometry plug-in (available in a separated setup) for database searches to identify molecules by monoisotopic mass and isotopic distribution.
  - Pockets: plug-in for the detection of the protein pockets. It uses the fpocket software developed by  Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery.
  - MDL Mol and SMILES copy to clipboard.
  - Possibility to set the probe radius when the volume or the volume diameter is calculated in the trajectory analysis tool.
  - Selection of nucleic acid backbone.
  - 10 bit output for each color channel (special graphic card and monitor are required).
  - Mopac interface updated.
  - Fix: HyperDrive DFT routines when executed by more than two threads.
  - AutoDock 4.2.3 is now included in the package (Win32, Linux x86 and Linux x64 versions).
  - New system variables: IsoDist, Smiles.
  - New extended commands: AtmInvChirality, BeginCalc, DbGetRowID, EndCalc, IsoDist, Score, SaveMolDlg, SelProx, SrfRename, TrjCurEne, Turbo, UndoPush, UnSelProx.
  - New scripts: AutoDock DLG to PDB Multimodel (convert the AutoDock DLG output to a PDB multimodel file), Protonation fix.c (fix the protonation state), SDF metadata extractor.c (extract the metadata from a SDF file), Stereoisomers.c (build all possible stereoisomers), Subset creator.c (create a database including a molecule subset from another database).
   
• Release ZZ 2.3.2 (11/11/2009)
  - GriDock: structure-based virtual screening software.
  - PDBQT multimodel trajectory loader (for AutoDock Vina).
  - Real time bump check.
  - Added the feature to save the calculated hydrogen bonds in CSV and DIF formats.
  - SQLite 3 database engine: it allows not only to store molecules, but also their properties that are calculated on-the-fly by VEGA ZZ for faster searches.
  - VEGA command line: now you can extract the frames from a trajectory file (-m Extract option).
  - SketchEl 2D molecular editor.
  - Unselect apolar hydrogens.
  - Calculation of isotopic distribution (isotopic pattern).
  - Support for NAMD 2.7.
  - Experimental Wine support. The setup is able to detect when VEGA ZZ is installed on a Linux/Wine system enabling specific optimizations.
  - Faster memory manager: it allows more responsive feedback.
  - Improved the CTorFind command. For this reason, the syntax was changed.
  - DMSO solvent cluster.
  - CHARMM 36 force field for small molecules.
  - Fix: error report when the Mopac calculation stops for an error.
  - Fix: IFF loader access violation when the file contains H-bond monitors.
  - Fix: Mopac extended command. Now select the correct executable version.
  - Fix: TrjWrite behaviour with invalid handles.
  - Fix: the AutoDock\Receptor.c script checks the maximum number to grid points for each dimension and sets it to 61 increasing the grid spacing in order to avoid to exceed the AutoDock/AutoGrid limits.
  - Fix: HyperDrive potential problem in the multithreading kernel (HD_WaitBarrier()) when a large number of CPUs is used.
  - GriDock manual and tutorial.
  - PowerNet plug-in: interface for Java applets.
  - New extended commands: Build3D, MenuEnable, MovieAdd, MovieClose and MovieCreate.
  - New scripts: AutoDock\Ki calculator.c (evaluate the Ki and the interaction energy of a ligand - receptor complex), AutoDock/Box calc.c (calculate sizes and center coordinates of the box used for docking studies), Build\Coordinate transformation.c (apply the transformation matrix to the atomic coordinates), Examples\Benzene.htm (build a benzene ring), Examples\Command console.htm (control VEGA ZZ by JavaScript), Movie\Movie Maker.c (create a move of a spinning molecule), Protein tools\Fred2 score.c (calculate the interaction score of a ligand - receptor complex).
  - Updated gl2ps library to 1.3.3.
   
• Release ZZ 2.3.1 (08/01/2009)
  - Added the support for Mopac 2009.
  - Fixed the resize problem of the select segment/molecule window.
  - Small bug fixes.
   
• Release ZZ 2.3.0 (11/12/2008)
  - Full support for NAMD 2 MD software with integrated graphic interface.
  - InChI loader and saver. Loading an InChI structure without the auxiliary data, it's automatically converted to 3D (VEGA ZZ only). Chirality and E/Z geometry is automatically checked and fixed if wrong.
  - AutoDock 4 PDBQT loader and saver.
  - AutoDock 4 DLG trajectory loader.
  - Mopac loader for geometry in Gaussian Z-matrix format.
  - Command line version: extraction of a molecule from a database (SDF and ZIP).
  - Chiral atom labels.
  - E/Z bond geometry monitors.
  - The PDB loader is now compatible with the alternate locations.
  - Remove apolar hydrogen.
  - Molar refractivity calculation (Ghose & Crippen method).
  - ChemSol plug-in for the calculations of solvation free energies.
  - Improved performances of the Molecule -> Fix menu function. Now it uses a graph-based routine to find the molecules.
  - PowerNet plug-in: added some on-line service (ChEBI, DrugBank, eMolecules, ERRAT 2.0, Google, KEGG Compound, KEGG Drug, MMsINC, NIST Chemistry WebBook, ProCheck, Prove, PubChem, Super Drug, VADAR, Verify3D and WHAT_CHECK).
  - New values in InfoXML format: chiralatms (list of the chiral atoms), chiralnum (number of chiral atoms), ezbonds (list of the bonds with E/Z geometry), gcmr (Ghose & Crippen molecular refractivity), eznum (number of bonds with E/Z geometry), hbondacc (number of H-bond acceptor atoms), hbonddon (number of H-bond donor atoms), realmols (real number of molecules), rings (number of rings), torflexnum (number of flexible torsions) and tornum (number of torsions).
  - PropKa: updated to the 2.0 release and the Windows x64 version built by gfortran.
  - New icons in the graphic interface.
  - New InChI copy special data types.
  - Fix: peptide builder window cut when the desktop dpi are more than 96.
  - Fix: Mopac loader and saver when the number of atoms is less than  three.
  - Fix: recognition of the Mopac Cartesian .arc files.
  - Fix: PDB saver writing the TER record with residue name length less than three characters.
  - Fix: tube rendering with big molecules and high spline resolution and hardware/software picture rendering.
  - Fix: measure selection in the trajectory analysis tool.
  - Added the chirality information in the IFF/RIFF file format.
  - New system variables: InChI, InChIAux, HbAcc, HbDon, Sequence, TotChiral, TotEZ, TotHeavyAtm, TotHydrog, TotRealMol, TotRing, VlogP.
  - New extended commands: CopyText.
  - New scripts: AutoDock\Ligand.c (prepare the current molecule to be docked by AutoDock 4), AutoDock\Receptor.c (prepare the current molecule to be the receptor usable by AutoDock 4), Calculation\Copy properties.c (copy some molecular properties to the clipboard), Claculation\Druglikeness.c (check the druglikeness of a molecule), Database\DrugBank SDF fix.c (fix the not standard SDF files from DrugBank), Trajectory\Anim maker.c (generate trajectories that can be rendered in video files), Trajectory\Automatic quenching.c (perform the automatic quenching of a MD trajectory. New version) and Trajectory\Dump energy.c (dump the energy of each frame in a trajectory file).

• Release ZZ 2.2.0 (10/04/2008)
  - Undo/redo functions.
  - Fasta loader with automatic conversion from 1D to 3D.
  - Mopac cartesian loader and saver.
  - PDB Large saver. The PDB Large file format was implemented in order to save molecules with more than 99999 atoms and is full compatible with the NAMD package.
  - Gromacs TRR trajectory loader & saver.
  - Peptide builder.
  - Protein secondary structure editing.
  - Bond length editing.
  - Added the automatic pair selection (Similar pairs and All pairs) in the similarity tool by a new popup menu.
  - Selection of the unconstrained atoms.
  - Automatic definition of the protein torsions (Omega, Phi and Psi) in the selection tool.
  - Added the -t and -u options to the command line version to change the protein secondary structure and to add the side chains to a protein.
  - Improved Mopac2007 support.
  - Automatic activation of the OpenGL V-sync. You don't need more to enable it in the graphic card control panel to improve the animation quality.
  - ISIS/Draw plug-in: now it checks if the hydrogens are already present in the ISIS/Draw structure and if this condition is true, no hydrogen is added. The Force add hydrog.  menu item allows to skip this check.
  - ISIS/Draw plug-in: the chirality is correctly kept during the molecule transfer from ISIS to VEGA ZZ.
  - New atom picking routine to avoid the performance issue of the OpenGL selection buffer implemented in the ATI drivers.
  - The Live CD Creator can install VEGA ZZ on a pen drive. Now it's possible to build a bootable CD with the VEGA ZZ plug-in for BartPE and PeBuilder.
  - Molecular docking tutorial with VEGA ZZ and Fred.
  - Added the support for the Asus Eee PC sub-notebook.
  - Fix: IFF loader & saver when the molecule contains centroids.
  - Fix: add hydrogen by bond order routine.
  - New script: PDB ren export.c (export the molecule in PDB format renumbering the atoms).
  - Updated VEGA SE screen saver (1.1.0.1).
  - VEGA On-line package and manual.

• Release ZZ 2.1.0 (10/10/2007)
  - CIF and mmCIF loader and saver.
  - MDL Extended Molfile (V3000) loader and saver.
  - Info XML saver.
  - mmCIF multi-model trajectory loader.
  - ISIS/Draw plug-in.
  - Stride plug-in.
  - Change bond dialog: added the function to replace the conjugated bonds with partial double bonds in aromatic rings.
  - The graphic interface is now COM Control 6.0 compliant.
  - Printable manual.
  - Added the -q option to the command line version to assign the bond order.
  - Fix: start-up problem of the latest Mopac 2007 releases.
  - Fix: small problem in the activation wizard.
  - Fix: client area in sizeable windows when Windows is configured with big fonts (> 96 DPI).
  - Fix: nanotube REBOL script.
  - New extended commands: Activate, FixArom, GraphAddEx, GraphType, UpdateLastFile.
  - New scripts: Database volume.c (calculate the volume of each molecule in the database), XYZ import.c (customizable XYZ loader).
  - Updated the CPU detection to recognize the new CPUs.
  - Updated the tutorial section.
  - VEGA SE screen saver.

• Release ZZ 2.0.8 (06/03/2007)
  - Conformational search (grid scan, random and Boltzmann jump).
  - Cluster analysis of the trajectory files (cluster by coordinates, by torsion and by torsion RMSD).
  - Mol2 multi-model trajectory saver.
  - X-Plor PSF loader.
  - ChemSol loader and saver.
  - CML 1.0 & 2.0 loader and saver.
  - PQR saver.
  - CHARMM 22 force field for AMMP.
  - Improved the rendering speed of solid surfaces with OpenGL 1.5 compliant graphic cards (2x time faster).
  - Mopac 2007 support (not included in the package).
  - PSF saver totally rewritten and new improper angle detection.
  - HyperDrive K8 for AMD Opteron, Athlon 64/FX and Sempron 64 CPUs.
  - 64 bit version of AMMP, ESCHER NG, InpMerge, PropKa, Top2Tem, Vega command line version, WarpBench, WarpGate, WarpKeyGen and WarpTel for Windows XP Professional x64 Edition, Windows Server 2003 x64 Editions and Windows Vista x64 Editions.
  - Slow motion function converting a trajectory to a video stream.
  - Gasteiger charges and the ATDL engine use the new parallel code.
  - ATDL template cache for a faster atom typing.
  - Added the possibility to compute manually the total charge in the Mopac dialog window.
  - PowerNet plug-in: script description feature.
  - Tutorials for most common molecular modelling problems.
  - Fix: Excel driver.
  - Fix: Gromos/Gromacs loading of very big files.
  - Fix: connectivity merge.
  - Fix: WarpGate access violation if an invalid host name is found in the configuration file.
  - Auto-installation utility for the license file (LicInst).
  - Updated the CPU detection to recognize the Intel Core 2 CPUs.
  - AMMP 2.2.0.
  - WarpGate 1.1.
  - New extended commands: AmmpSetFF, AmmpUpdateFreq, CTorClear, CTorGet, CTorFind.
  - New system variable: TotCTor.
  - New scripts: Database logP.c (calculate the logP for each molecule in the database), SDF export.c (export a trajectory in a SDF database), Dump backbone torsions.c (dump the phi and psi backbone torsion values).
  - InpMerge: utility to merge the CHARMM/NAMD parameter files.
  - Italian localization of the setup procedure.
  - Updated the gl2ps library to 1.3.2.
  - Updated the libbzip2 library to 1.0.3.
  - Updated the ziplib library to 1.0.1.
  - Updated the zlib library to 1.2.3.
  - Demo music remastered with surround effects.

• Release ZZ 2.0.7 Web Edition (18/09/2006)
  - It contains the same improvements of the Euro QSAR 2006 Edition, but it's designed for the Web distribution.

• Release ZZ 2.0.7 Euro QSAR 2006 Edition (10/09/2006)
  - Molecular mechanics provided by AMMP (Another Molecular Mechanics Program).
  - Host control system for remote jobs.
  - AMMP loader and saver.
  - CPMD XYZ loader and saver.
  - Mol2 and MDL Mol multi-model trajectory loader.
  - AMMP - MoM atomic charge calculation.
  - SVG image output.
  - Fix: Gl2vrml library memory leak.
  - Fix: PROPKA bug when the path of temporary directory contains dots.
  - Fix: RIFF/IFF charge and potential chunk bug.
  - Fix: client area reduction of resizable windows when the window title bar height is greater than 14 pixels.
  - Fix: Connectivity merge.
  - Fix: Excel driver.
  - Fix: SDF database engine.
  - Fix: Lock of the HyperDrive parallel threads after preferences change.
  - New extended commands: AmmpSend, AmmpSendMol, AmmpStartCalc, SoundEffects.
  - New system variable: SoundEffects.
  - New scripts: 2D to 3D.c (convert a structure from 2D to 3D), Aromaticity fix.c (Fix the bond order in aromatic rings), CSSR SOMFA export.c (export the molecule in SOMFA readable format), Database 2D to 3D (convert a database from 2D to 3D), Database to 0D.c (convert a database from nD to 0D), Dipole.c (compute the dipole momentum with AMMP), GraphApp demo.c (Demo of the GraphApp GUI library), InChI convert.c (IUPAC InChI converter), Interaction analysis.c (evaluate the interaction energy between two molecules), Neural network.c (use the AMMP's neural network to reconstruct the 3D geometry), Rigid docking.c (genetic algorithm rigid docking), Zero coord.c (Place the atoms at the specified coordinates).
  - WarpBench parallel linpack benchmark.
  - WarpGate encrypted tunnelling service for Linux and Windows.
  - WarpKeyGen encryption key generator.
  - WarpTel encrypted telnet server for Windows.
  - Updated the Gl2ps library to 1.3.1.
  - Updated REBOL/View to 1.3.2.
  - Live ! distribution. It doesn't requires the installation and VEGA runs directly from the CD-Rom drive.

• Release ZZ 2.0.6 (28/02/2006)
  - PROPKA plug-in for protein pK_a calculation (thanks to Jan H. Jensen).
  - Added the capability to add the atom charges using a fragment/residue database containing pre-computed charges.
  - Gaussian input loader and saver.
  - Gaussian output loader.
  - RIFF, RIFF 64 bit and IFF 64 bit molecule/trajectory loader and saver.
  - New algorithm based on the bond order to add hydrogens. This is useful for databases and 2D structures.
  - The DCD reader and writer is now compatible with the trajectories containing the cell information.
  - Add fragment with automatic residue number increment.
  - Preferences dialog box.
  - Introduction to the VEGA Graphic Language (VEGA GL).
  - Added Edit -> Remove -> Graphic objects menu item.
  - Updated PDB download for the new RCSB Web site.
  - Fix: molecule view loading files overriding the Z-clip plane.
  - Fix: Mopac 7 bug due to g77 3.4.2.
  - New extended commands: VglBegin, VglColor, VglColorRGB, VglDisable, VglEnable, VglGroupBegin, VglGroupEnd, VglGroupHide, VglGroupRemove, VglGroupShow, VglEnd, VglInit, VglLabel, VglLineWidth, VglLoadIdentity, VglNormal, VglPointSize, VglPopMatrix, VglPushMatrix, VglRadius, VglRadius3, VglRotate, VglScale, VglTranslate, VglVertex.
  - Top2tem: utility to convert CHARMM topology files (.top) to VEGA template files for charges (.tem).
  - Updated SendVegaCmd to 2.6.

• Release ZZ 2.0.5 (5/12/2005)
  - C script engine based on Tiny C compiler.
  - Mopac 7.01-4 is now included in the package.
  - Ramachandran plot plug-in (RamaPlot).
  - Customizable Cartesian axis.
  - VRML 2.0 and POV-Ray  output (powered by Gl2Vrml library).
  - New in the database explorer: support for the file drag & drop, molecule list save and clipboard copy functions.
  - Selectable multisample anti-aliasing.
  - Configuration of human interface devices (HID).
  - Fix: small SDF database remove molecule bug.
  - Fix: trajectory gyration radius calculation.
  - Fix: dotted PSA surface calculation apolar and polar area value.
  - Fix: access violation saving the surfaces.
  - Fix: H-bond donor surface calculation.
  - Fix: removed the artefacts in transparent surface visualization.
  - Fix: HyperDrive handle release in SMP mode.
  - Fix: bond angle adding the hydrogens to the water molecules.
  - Fix: snapshot corruption with ATI graphics card when the multisample anti-aliasing is enabled.
  - Fix: first atom skipping in xyz loader.
  - New scripts: ActiveSync VRML send.c (convert the molecule to VRML and send it to the mobile device using ActiveSync), CML export.c (export the current molecule in Chemical Markup Language), CSV export.c (export the current molecule in Comma Separated Values format), Color RasMol.c (color the molecule using the RasMol color scheme), Color VMD.c (color the molecule using the VMD color scheme), E-mail PDB send.c (send a molecule in PDB format as e-mail attachment), Electrostatic energy.c (evaluate the electrostatic energy), HIS protonation.c (check the histidine protonantion state calculating the hydrogen bond energy), IrDA VRML send.c (convert the molecule to VRML and send it to the mobile device over an infrared link), Move hydrogens to end.c (move the hydrogens at the end of the atom list), Ramachandran.c (perform the Ramachandran analysis of a MD trajectory).
  - New extended commands: EneParGet, EneParSet.
  - New system variables: MsAA, WinHandle.
  - How-to manual section.
  - Updated ClustalX to 1.8.3.
  - Updated the Gl2ps library to 1.2.6.
    
  
• Release ZZ 2.0.4 (29/06/2005)
  - Added the capability to read Mopac 2000 .arc files.
  - Fix: EAccessViolation error with non-European Windows versions.
  - Fix: Mol2 loader for FLEXX files.
    
  
• Release ZZ 2.0.3 (21/06/2005)
  - Automated bug report procedure.
  - VEGA ZZ is now compatible with Windows 95.
  - Added the capability to un/select and remove waters without hydrogens.
  - Fix: SrfCalc command.
  - Fix: ESCHER NG output recognition.
  - Fix: potential division by zero loading DCD files.
  - Fix: .car file merge.
  - New extended commands: Volume.
  - New system variables: FlexTor.
  - All DLLs are rebuilt with MinGW 3.1, because the release 4.0 generates wrong SSE code for the Pentium 4 target.
  - REBOL/View 1.3 script engine.
  
  
• Release ZZ 2.0.2 (24/05/2005)
  - Trajectory file converter with cut/skip frame and atom remove capabilities.  The supported formats are CHARMM/NAMD DCD, PDB and Gromacs XTC.
  - Video stream encoder: the MD trajectory can be converted into a video animation using the Microsoft Multimedia System (AVI file format) or the built-in MPEG-1/2 encoder (mpg and VOB files).
  - Exclusion of atoms in the trajectory analysis.
  - TINKER XYZ loader.
  - Added the support for DCD trajectories with atom fixing.
  - Hydrogen bond finder and energy evaluation with CHARMM force field.
  - H-bond acceptor and donor surface calculation. 
  - Selection of the superficial atoms that are solvent accessible.
  - The atoms can be colored by the property to accept or donate H-bonds.
  - Graph Editor: DFT frequency spectrum analysis, DFT high frequency noise reduction, derivative calculation and label change capability.
  - Automatic selection of the MOPAC executable based on the number of heavy atoms and hydrogens. MOPAC versions for molecules with 50/100/300 heavy atoms and 100/200/600 hydrogens are included in the package.
  - Added the anti-alias function (4x and 16x) when you save images with the software rendering engine.
  - Added Inherit residue name option in the Add fragment/s dialog.
  - The default window refresh is now set to slow mode for more graphic card compatibility.
  - Added the possibility to change the animation frame rate and the animation base timing.
  - Removed the 2 Gb file size limit of trajectories and databases. The theoretical maximum file size is now 16 Exabytes.
  - Increased performances of the database engine. Now it's possible to manage SDF files containing millions of structures.
  - Fix: Graphic corruption for non-Matrox cards.
  - Fix: Broto/Moreau template. Now the phenolic oxygen atom type is correctly assigned.
  - Fix: Ring detection in the add hydrogens function.
  - Fix: csv, Insight and Quanta surface save procedure.
  - Fix: MDL mol bond type attribution.
  - Fix: Mol 2 loader element recognition.
  - Fix: access violation closing the console.
  - Fix: access violation closing the Graph Editor.
  - Fix: access violation closing databases.
  - Fix: TIFF image saver.
  - Fix: Windows 9x license management.
  - New scripts: Aminoacid selector.r (show the aminoacids by selection and/or chemical/physical properties), Benzene.bat (build a benzene ring using the extended commands), Enantiomerizer.r (convert a trajectory file into the enatiomer one), Ftp put.r (copy a molecule from the workspace to a remote host via FTP), Graphite.r (build graphite planes), Nanotube.r (build nanotubes), Remove apolar hydrogens.r.
  - New extended commands: AssignBndOrd, AtmAdd, AtmBeginUpdate, AtmBond, AtmDelete, AtmEndUpdate, AtmFind, AtmGet, AtmSet, ConnBuild, ConnDestroy, Cursor, DbPut, GraphActivate, GraphBeginUpdate, GraphDerivative, GraphEndUpdate, GraphExcel, GraphMaximize, GraphMinimize, GraphNR, GraphPrint, GraphRestore, GraphSpectrum, GraphToClip, TrjClose, TrjCreate, TrjSave, TrjWrite.
  - New system variables: Formula, ConDocked, Mass.
  - Updated the FAQ section.
  
  
• Release ZZ 2.0.1 (20/12/2004)
  - Now it's possible to export the molecules directly in Microsoft Excel.
  - Slice selector.
  - The Graph Editor can export the data to Microsoft Excel.
  - Fix: corruption of Z-buffer in stereo view (active glasses).
  - Fix: Windows 9x host detection.
  - Fix: ESCHER NG surface loader.
  
  
• Release ZZ 2.0.0 (15/11/2004)
  - Introduction of the HyperDrive technology for an incredible computational speed thanks  to its linarized and prallelized  code. It uses the full power of your multiprocessor system !
  - The surface calculation is included in the HyperDrive library. The computational speed is increased to  about 40x.
  - The trajectory analysis takes full advantages of multiprocessor systems with a tremendous calculation speed-up.
  - The HyperDrive includes fast linear routines for the topology calculation and so the PSF file generation is about 20 time faster.
  - The MLP/Virtual logP calculation is now included in all VEGA versions. 
  - Load/save CRT crystallographic files used at the Indiana University Molecular Structure Center (IUMSC).
  - Gyration radius calculation (Info & trajectory analysis).
  - Fix: MEP surface calculation.
  - Added the capability to read Mac ASCII files without conversions. 
  
  VEGA ZZ 2.0.0 updates:
  - New graphic interface.
  - Draggable console, menu and tool bars.
  - Improved graphic performances thanks to the new lighting engine and the possibility to mix the display modes.
  - Fast solid and mesh surface calculation (HyperDrive powered).
  - Enhanced surface color capabilities with customizable gradients.
  - Multiple surface management.
  - Tube and trace visualization modes.
  - Customizable fonts.
  - Support for stereo devices (shutter and anaglyphic glasses).
  - Support for distributed OpenGL rendering (WireGL). 
  - Color settings. 
  - Swap bonds and change angle functions.
  - Improved mouse control and extended move function.
  - Add aminoacid side chains function.
  - Improved functions in solvent cluster dialog.
  - Enhanced image rendering capabilities: now it's possible to choose  the rendering engine, the image size and the effects/filters to apply.
  - Vector rendering: you can export  the view in LaTex, PDF, PostScript and Encapsulated PostScript.
  - New print engine: now it's possible to hard copy the OpenGL window at full printer resolution for an incredible quality.
  - Check for aminoacid chirality, peptidic bond geometry (cis/trans), missing aminoacids and ring intersections.
  - Add atom and Add fragment dialogs: added the possibility to choose where to put  the atoms in the atom list.
  - Expanded configuration parameters for RMSD calculation.
  - Added Data Interchange Format (DIF) loader and saver in the GraphEd. This feature allows better data import in Microsoft Excel.
  - Now the GraphEd allows to select the energy type to read from NAMD output.
  - New extended commands: BackColor, Light, LightAmb, LightAmbColor, LightCur, LightCurDifCol, LightCurEn, LightCurPos, LightCurSpecCol, LogoPos, LogoScale, MatShiny, MatSpecular, MatVectSpec, MeshLoad, MusicPlay, MusicStop, mTbStandard, mTbTools, Shutdown, SrfAlpha, SrfAlphaVal, SrfColorGrad, SrfCur, SrfDotSize, SrfGrad, SrfGradAutoRng, SrfGradRange, SrfRemove, SrfRemoveAll, SrfVisible, TraceProp, TubeProp.
  - New system variables: BackColor, LastFileName, SaveDir, Light, LightAmb, LightAmbColor, LightCur, LightCurEn, LightCurDifCol, LightCurSpecCol, LightCurPos, LogoPos, LogoScale, MatShiny, MatSpecular, MatVectSpec, SrfCur, SrfName, SrfType, SrfVisible, SkyBoxEnabled, SkyBoxName, SkyBoxOffsetX, SkyBoxOffsetY, SkyBoxRotX, SkyBoxRotY, SkyBoxRotZ, TotBond, TotChain, TotImp, TotRes, TotSeg, TotSrf, TotSrfDot, TotSrfTri, TotTor.
  - The source code is now compiled with Borland C/C++ Builder 6.
  - More computational power thanks to the Borland fastmath library.
  - WinDD 1.5. 
  
  
• Release 1.5.1 (16/12/2003)
  - Chem3D loader.
  - Accelrys archive file (.arc) support in the trajectory analysis.
  - Capability to add the hydrogens.
  - RMSD calculation in trajectory analysis.
  - CHARMM lipid and GRID force field templates.
  - POPC lipid bilayer cluster in crystal and solid phase. 
  - Fix: energy interaction evaluation.
  - Fix: PSF X-Plor file saver. Now is full compatible with NAMD.
  - Fix: NAMD 2.5b2 & 2.5 output format detection.
  
  Windows/OpenGL updates:
  - ESCHER NG and ESCHER NG Plugin: protein-protein and DNA-protein docking system.
  - Database engine for directory, sdf and zip files.
  - Complete 3D molecular editor with fragment libraries (Add fragment function).
  - Multiple workspaces.
  - Remove residue/s dialog box.
  - Molecule place dialog box.
  - Added the capability to show the worst energy interacting residues with biomacromolecule (Evaluation of the interaction).
  - Fix/merge molecules.
  - Multiple Mini Editor and Graph Editor windows.
  - Now the centroids can be updated dynamically or kept fixed.
  - The residue renumbering is now available for all atoms and for the selected atoms only.
  - Fixed single atom remove function.
  - Changed the keys to control the mouse function (R = rotation, S = scale, T = translation).
  - New extended commands: AddIons, AddHydrog, DbClose, DbCreate, DbGet, DbGetId, DbInfo, DbOpen, GraphSetCur, RemAtoms, WksChange, WksLock, WksNew, WksNext, WksPrev, WksRem, WksRemAll, WksRemCur, WksSetName, WksUnLock.
  - New system variables: GraphID, WksCurName, WksCurNum, WksTot.
  - Updated Fmod DLL to 3.70.
  - New demo music "Rainstorm Cloudburst Mix" by Chris Hülsbeck.
  
  
• Release 1.5.0 (24/06/2003)
  - PDB 2.2 loader and saver.
  - Experimental PSF X-Plor topology saver.
  - Improved GAMESS support. Now VEGA reads the minimized structures and the atomic charges.
  - Added the capability to read the connectivity and the bond types of Alchemy, CSSR, MDL Mol,  Mol2, PDB (including all subformats), QMC and IFF file formats.
  - Ultra fast connectivity calculation routine.
  - Now IFF and PDB file formats support the atom constraints.
  - Read & write substructure record in Mol2 file format.
  - New trajectory file formats: Quanta conformational search (CSR), ESCHER Next Generation solutions.
  - Added the lipole measure (Broto & Moreau, Ghoose & Crippen) in the trajectory analysis.
  - Support of multiple chains in IFF file format.
  - Bond, CFF91, CHARMM 22 for nucleic acids, CHARMM 22 for proteins, H-bond, MM2, MM3, force field templates.
  - The atom type length is expanded from 4 to 8 characters trough the 64 bit technology (e.g. Tripos atom types). 
  - Added acetone, ammonia, chloroform, dicloromethane, formaldehyde, methane, methanol octanol-water solvent clusters.
  - New specifications for IFF (1.3), PDBA (1.1), PDB FAT (1.1) file formats.
  - Fix: ATDL engine.
  - Fix: IFF multi-segment saver.
  - Fix: trajectory analysis water exclusion routines.
  - Fix: angle between two planes in trajectory analysis.
  - Win32: basic 3D molecular editor with add, remove, change atom capability and bond manipulation (add, remove, change, connectivity rebuilder and bond type finder).
  - Win32: molecular similarity toolbox (molecular superimposition).
  - Win32: change torsion dialog box.
  - Win32: solvent cluster builder.
  - Win32: add ions function (based on Sodium source code developed by Alexander Balaeff).
  - Win32: merge file function. You can merge two files specifying the parts to keep or discard (e.g. coordinates, atom types, atomic charges, etc).
  - Win32: ClustalX plugin.  It allows to integrate molecular biology tools (ClustalX and NJPlot) in the VEGA environment.
  - Win32: atom constraints dialog box for dynamics simulations (e.g. NAMD).
  - Win32: 3D interactive monitors for distance, angle, torsion, angle between two planes.
  - Win32: world relative translation and rotation of each molecule.
  - Win32: open/save in selection tool (trajectory analysis).
  - Win32: select molecules and select segments dialogs.
  - Win32: remove molecules and remove segments dialogs.
  - Win32: remove invisible atoms.
  - Win32: fix/merge segments.
  - Win32: color by fixing value.
  - Win32: labels by fixing value, residue, residue name and residue number.
  - Win32: show/hide atoms by molecule and improved atom selection.
  - Win32: invert Z coordinates function in order to obtain the enantiomer.
  - Win32: apply 3D transformation to coordinates.
  - Win32: now it's possible apply the force field and the atomic charges to all atoms, and to active (visible) atoms only.
  - Win32: event logging in PowerNet plugin.
  - Win32: changed extended commands: Charge, ForceField.
  - Win32: new extended commands: Angle, Distance, Merge, PlaneAng, Torsion, TrjGraphEne.
  - Win32: new system variables: TotActAtm, TotMol.
  - Win32: updated DevIL DLLs to 1.6.5.
  - Win32: new demo music "Giana Sister (Machinae Supremacy Remix)" by Chris Hülsbeck.
  
  
• Release 1.4.3 (11/12/2002)
  - Alchemy loader & saver.
  - MDL Molfile saver.
  - CSV and Raw surface format.
  - Gromacs .xtc support for the trajectory analysis.
  - Multi-model PDB support for the trajectory analysis.
  - ILM calculation in the trajectory analysis.
  - The IFF file format was expanded in order to support the surface maps.
  - Win32: new geometry transformation engine.
  - Win32: added By segment coloring method.
  - Win32: surface calculation for selected atoms.
  - Win32: trajectory analysis for selected atoms.
  - Win32: interactive selection of the conformations trough the graph editor.
  - Win32: added the Data De/compressor Engine support in the graph editor.
  - Win32: now the graph editor supports Gromacs log files.
  - Win32: REBOL/View instead of REBOL/Core scripting language. 
  - Win32: new extended commands (BioDock, GraphAdd, GraphCalc, GraphClose, GraphDelete, GraphGet, GraphLabelX, GraphLabelY, GraphLoad, GraphNew, GraphOpen, GraphSave, GraphSet, GraphTitle, GraphWin, MonitorPower).
  - Win32: new system variables (CPUs, GLRenderer, GLVendor, GLVersion, GraphLabelX, GraphLabelY, GraphPoints, GraphPosX, GraphPosY, GraphSizeX, GraphSizeY, GraphTitle, GraphVisible, TmpFile, TmpDir).
  - Win32: WinDD 1.4.
  - Win32: new demo music by Chris Hülsbeck.
  
  
• Release 1.4.2 (03/09/2002)
  - Updated the Gasteiger-Marsili charge attribution.
  - GAMESS output loader.
  - Fix: mol2 sever (now the am bond order is correctly assigned).
  - Win32: PowerNet plugin: TCP/IP protocol and PDB interface.
  - Win32: the REBOL scripting language is now included in the package.
  - Win32: edit atom, residue and chain properties.
  - Win32: console command history.
  - Win32: smart move rendering option.
  - Win32: new extended commands (ChDir, ColorIdDlg, ColorRgbDlg, ConClrHist, ConCls, ConSave, ConSet, ConWin, DirDlg, ErrMsg, LogOff, MessageBox, MainWin, MiniEd, Mopac, OpenDlg, SaveDlg, SaveImg, ShutDown, SrfCalc, SrfColor, SrfColorBy, Text).
  - Win32: new system variables (ConBufSize, ConHistSize, ConPosX, ConPosY, ConSizeX, ConSizeY, ConVisible, CpuFeatures, CpuName, CpuType, CpuVendor, CurDir, GlassWin, IsRunning, Os, OsFamily, ScreenDepth, ScreenX, ScreenY).
  - Win32: TurboPack for AMD Athlon/Duron and for Intel Pentium 4.
  - Win32: new demo song by Gianna Pica.
  - Win32: updated Fmod DLL to 3.6.
  
  
• Release 1.4.1 (03/06/2002)
  - GAMESS cartesian file loader and saver.
  - Fix: HyperChem .hin loader.
  - Fix: XYZ detection.
  - Fix: Insight surface loader.
  - Fix: generation of solvent cluster.
  - Fix: Pentium III-M CPU detection.
  - Win32: interaction energy evaluation for the analysis of the docking results.
  - Win32: new console with direct command interface.
  - Win32: advanced cut, copy & paste routines.
  - Win32: Predator plugin interface.
  - Win32: glass windows (Windows NT/2000/XP only).
  - Win32: PLUGINGET command added.
  - Win32: Dhrystone plugin 1.1.
  - Win32: updated DevIL DLLs to 1.3.1.
  
  
• Release 1.4.0 (15/04/2002)
  - MDL Mol file loader.
  - Improved IFF file format (new chunks).
  - Extended command line interface for language scripting.
  - Return code handler.
  - Fix: Biosym archive 3 (.car) loader now reads the element column.
  - Fix: mol2 hack for Insight generated mol2 files.
  - Fix: mol2 saver.
  - Manual: added Frequently Asked Question (FAQ) page.
  - Win32: atom picking and interactive measures/selection (atom, distance, angle, torsion and angle betwee two planes).
  - Win32: plugin system to expand the VEGA capabilities.
  - Win32: Dhrystone Test plugin (tstdhry.dll) to test the CPU performance.
  - Win32: joystick control.
  - Win32: color requester.
  - Win32: customizable atom selection.
  - Win32: some new commands can be send trough the standard window port, in order to interpret complex command sequences.
  - Win32: now the trajectory animation is compatible with the new refresh mode.
  - Win32: the selection tool for trajectory analysis supports the atom picking.
  - Win32: the trajectory files can be opened directly with File -> Open menu item.
  - Win32: dynamic loading for devil.dll, fmod.dll, ilu.dll, ilut.dll, libbz2.dll, z32.dll and zlib32.dll.
  - Win32: VEGA selects the DLLs with the optimizations for the installed CPU.
  - Win32: new menu items: Help -> Last error and Display -> Select -> None.
  - Win32: new demo music by Chris Hülsbeck.
  
  
• Release 1.3.2 (6/11/2001)
  - Now VEGA can read the DCD files in little or big endian format without conversion.
  - Added the PDB ATDL (PDBA) file support (read and write).
  - Fix: Fasta  saver.
  - Win32: more mouse controls trough the middle button and the wheel.
  - Win32: added Select menu item to show/hide a part of a molecule.
  - Win32: added Color -> By residue, Color -> By chain and Color -> By charge menu item.
  - Win32: new Save Image output formats (Gif, Jpeg, OpenIL, PCX, PNG, PNM, Raw, SGI, Targa and Tiff).
  - Win32: added the View Settings dialog box.
  
  
• Release 1.3.1 (02/10/2001)
  - Win32: improved CPK visualization.
  - Win32: added VdW Dotted and Liquorice visualization modes.
  - Win32: some configuration parameters (window size and position, menu checkmarks, etc) are stored when the program is closed.
  - Win32: menu history of the opened files.
  - Win32: added window popup menu to resize the main.
  - Win32: more than one VEGA session can be opened at the same time.
  - Win32: drag & drop function to open the molecules.
  - SendVegaCmd can control more than one VEGA session.
  - SendVegaCmd asyncronous mode.
  
  
• Release 1.3.0 (13/09/2001)
  - Data De/Compressor Engine updated: now you can pack the output in BZip2, GZip, PowerPacker (Amiga only) and Z-Compress.
  - ILM (Molecular Hydropathicity Index) surface calculation.
  - Polar surface area calculation (PSA).
  - HyperChem HIN loader.
  - Added charge and force field check in CVFF energy evaluation.
  - Connectivity routine rewritten and more fast.
  - Surface routines totally rewritten for load/save operations.
  - DCD analyzer can load both CRD or MSF packet files.
  - Water remove option (-w) in trajectory analysis.
  - Fix: gromos loader/saver.
  - Fix: multiple PDBF loading.
  - Fix: routine for ring search.
  - Fix: CHARMm force field template.
  - Fix: a little bug in msf loader.
  - Fix: Mopac loader more compatible.
  - Fix: solvent layer calculation.
  - Linux: first official release.
  - Unix: fixed water detection routine.
  - Win32: Graphic interface with 3D OpenGL output.
  - Win32: fixed program path detection.
  - Win32: fixed CTRL+C execution halting.
  - Win32: setup program for easy insallation.
  - Win32: WinDD Data Decompressor software included in the package.
  
  
• Release 1.2
  - Data Decompressor Engine with BZip2, GZip, PowerPacker and Z-Compress compatibility.
  - Language localization trough the IFF catalog system and localization package.
  - Loader for Sybyl .rgn files.
  - The environment variable VEGADIR is not more needed for Amiga and Win32 versions.
  - COMFA field calculation: lypophilic.
  - CHARMm force field template fixed.
  - Biosym surface atom label fixed.
  - Amiga: fixed some endian problems.
  - Sources: multiple test script
  - Sources: Z32, Z and Bzip2 libraries and DLLs.
  - Sources: StripCR utility with patter matching
  - Win32: added pattern matching.
  - Win32: fixed msf saver.
  - Win32: fixed remove hydrogens (-r) and remove waters (-w) functions.
  
  
• Release 1.1a
  - Fixed an heavy bug in PDB loader and saver.
  - Mol2 filter more compatible.
  
  
• Release 1.1
  First public release.
  
  
• Release 1.0
  Only for internal use.

26. How to cite VEGA and VEGA ZZ

If you use VEGA and VEGA ZZ for your research, you agree to cite the publications detailing the original methods and reference data used, as well as one of the specific papers:

A. Pedretti, A. Mazzolari, S. Gervasoni, L. Fumagalli, G. Vistoli
"THE VEGA SUITE OF PROGRAMS: AN VERSATILE PLATFORM FOR CHEMINFORMATICS AND DRUG DESIGN PROJECTS"
Bioinformatics, Vol. 37(8) 1174-1175 (2021).
DOI: 10.1093/bioinformatics/btaa774

 

Other articles on VEGA an related programs are available here.

Electronic documents should include a direct link to the Drug Design Lab home page:

http://www.ddl.unimi.it

or to VEGA ZZ Web site:

http://www.vegazz.net

27. Acknowledgements

• Ahmed H.M.Solieman (some C-scripts).
• Alexander Balaeff (Soudium software).
• Artifex Software, Inc (MuPDF).
• Bernard Testa et al. (Virtual logP - CLIP).
• Carl Sassenrath ( Language).
• Christophe Geuzaine (GL2PS library).
• Daniel M. Lowe, Peter T. Corbett, Peter Murray-Rust, Robert C. Glen (OPSIN).
• Denton Woods ( Image Library).
• Dimitrij Frishman & Patrick Argos (Predator, STRIDE).
• Diomidis Spinellis, James A. Woods,  Spencer Thomas and Joseph Orost (compress source code).
• Doug Lea (dlmalloc).
• Fabrice Bellard ( Tiny C compiler).
• FireLight Multimedia ( FMOD Sound/Music API).
• Frank Eisenhaber (NSC subroutine).
• Frans van Hoesel (Xdrf library).
• Free Software Foundation (GNU packages ).
• Garrett M. Morris, David S. Goodsell, Ruth Huey, William Lindstrom, William E. Hart, Scott Kurowski, Scott Halliday, Rik Belew, Arthur J. Olson (AutoDock).
• GGA Software Service (Indigo Toolkit and Ketcher 2D editor).
• Igor Filippov (OSRA).
• James Stewart (MOPAC).
• Jan Florián and Arieh Warshel (ChemSol 2).
• Jan H. Jensen, Andrew D. Robertson, Hui Li, David M. Rogers (PROPKA).
• Jean-loup Gailly and Mark Adler (GZip and Zlib).
• Jordan Russell (Inno Setup Compiler).
• Julian Seward (Bzip2 and libbz2).
• Julie Thompson, Toby Gibson, Des Higgins (ClustalX).
• Krzysztof Kowalczyk (Sumatra PDF and custom MuPDF library) .
• Lachlan "Loki" Patrick (GraphApp library).
• Nathan Baker, J. Andrew McCammon and Michael Holst (APBS).
• Manolo Gouy (NJPlot).
• Manuela Helmer Citterich, Gianni Casareni, Gabriele Ausiello (ESCHER docking system).
• Marcin Orlowski (FlexCat catalog compiler).
• Maurizio Vacca and Enrico Antongiovanni (3G Electronics).
• Michele Puccini (ClassX Development).
• Michel Leunen (TBrowseDlg BCB component).
• Michele Parrinello (CPMD software).
• Mummit Khan, Danny Smith, Ernie Boyd and theirs developer groups (Minimalist GNU for Windows).
• Oleg Trott (AutoDock Vina).
• Paul Bourke (several 3D graphic gems).
• Path Hanrahan, Greg Humphreys, Ian Buch, Matthew Eldridge, Matthew, Everett, Christopher Niederauer of Stanford University Graphics Lab (WireGL).
• Persistence of Vision Team, Persistence of Vision Raytracer Pty. Ltd. and Christopher Cason (Persist of Vision Ray Tracer).
• Renxiao Wang (X-Score).
• Robert W. Harrison (AMMP molecular mechanics software).
• Roberto G. A. Veiga, Instituto de Física - Universidade Federal de Uberlândia (UFU) - Brazil (Nanotube code).
• Thomas E. Exner (PLANTS software).
• Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery (fpocket package).

Special thanks to all VEGA testers:

• Alessandro Contini.
• Deborah E. Shalev.
• Guillermo A. Morales.
• Joshua D. Moore.
• Kim Henrich.
• Laura De Luca.
• Robert Paul Bywater.
• Stephen Lawrence.
• Tom Scior.

All people unintentionally not mentioned in this document, please don't offend.

No endorsement of any hardware of software should be inferred

APPENDIX A - Gasteiger-Marsili parameters

All this parameters are included in GASTEIGER.tem file stored in Data directory.

#TemplateCharge Gasteiger

; *************************************************
; ****              VEGA Template              ****
; ****  Gasteiger-Marsili template for charges ****
; *************************************************

; Ref. Tetrahedron, 36, 3219, 1980
;      Croat.Chem.Acta, 53, 601, 1980

#Title Gasteiger-Marsili charges

; Type        a        b        c        d      Charge
; =====================================================
  H          7.17     6.24    -0.56    12.85     0.000000
  HOS3      15.00     6.24    -0.56    20.68     0.000000
  C3         7.98     9.18     1.88    19.04     0.000000
  C2         8.79     9.32     1.51    19.62     0.000000
  CS2        7.35     1.40     0.30     8.40     0.000000
  C1        10.39     9.45     0.73    20.57     0.000000
  N3        11.54    10.82     1.36    23.72     0.000000
  N2        12.87    11.15     0.85    24.87     0.000000
  N1        15.68    11.70    -0.27    27.11     0.000000
  O3        14.18    12.92     1.39    28.49     0.000000
  O2        17.07    13.79     0.47    31.33     0.000000
  OS4E      13.00     5.00     1.50    18.00     0.000000
  F         14.66    13.85     2.31    30.82     0.000000
  Cl        11.00     9.69     1.35    22.04     0.000000
  Br        10.08     8.47     1.16    19.71     0.000000
  I          9.90     7.96     0.96    18.82     0.000000
  S2        10.50     1.80     2.00    13.80     0.000000
  S3        10.14     9.13     1.38    20.65     0.000000
  P          8.90     8.32     1.58    18.10     0.000000
  Du         0.00     0.00     0.00     1.00     0.000000
  SO2        7.00     1.40     0.30     8.40     0.000000
  SO4        5.40     1.40     0.30     6.40     0.000000
  OS2       18.00     2.00     0.20    20.00     0.000000
  CSO2      12.00     1.80     2.00    13.80     0.000000
  NSO2      13.00     1.80     2.00    14.80     0.000000

; Atoms with localized partial charge

  CN        10.39     9.45     0.73    20.57    -0.500000
  S-        10.14     9.13     1.38    20.65    -1.000000
  SO1       10.14     9.13     1.38    20.65     1.000000
  S+         5.10     3.80     0.50    20.65     1.000000
  SO3H       5.14     5.13     0.38    10.65     3.000000
  SO3-       5.14     5.13     0.38    10.65     2.000000
  NC        15.68    11.70    -0.27    27.11    -0.500000
  O-        17.07    13.79     0.47    31.33    -0.500000 
  OP        17.07    13.79     0.47    31.33    -0.500000 
  OP=       17.07    13.79     0.47    31.33    -0.666667
  OS1       17.07    13.79     0.47    31.33    -1.000000
  OS3       17.07    13.79     0.47    31.33    -1.000000
  OS4       17.07    13.79     0.47    31.33    -0.333334

; Guanidine group:

  CG         8.79     9.32     1.51    19.62     0.040000
  NG        17.07    13.79     0.47    31.33     0.320000

  N3+       11.54    10.82     1.36    23.72     1.000000
  NP+       11.54    10.82     1.36    23.72     1.000000
  NI+       11.54    10.82     1.36    23.72     0.500000
  
  PN        11.54    10.82     1.36    23.72     0.000000 
  P=         8.90     8.32     1.58    18.10     0.010000

  Na         0.00     0.00     0.00     1.00     1.000000
  K          0.00     0.00     0.00     1.00     1.000000
  Ca         0.00     0.00     0.00     1.00     2.000000
  Mg         0.00     0.00     0.00     1.00     2.000000
  Mn         0.00     0.00     0.00     1.00     2.000000
  Fe         0.00     0.00     0.00     1.00     2.000000
  Zn         0.00     0.00     0.00     1.00     2.000000
  Co         0.00     0.00     0.00     1.00     3.000000
  Cr3+       0.00     0.00     0.00     1.00     3.000000
  F0         0.00     0.00     0.00     1.00    -1.000000
  Cl0        0.00     0.00     0.00     1.00    -1.000000
  Br0        0.00     0.00     0.00     1.00    -1.000000
  I0         0.00     0.00     0.00     1.00    -1.000000

APPENDIX B - VEGA prefs file

This is an example of VEGA prefs file. This file must be placed in Data directory.

; ********************************************
; ****      VEGA V3.2.3 - Preferences     ****
; **** (c) 1997-2023, Alessandro Pedretti ****
; ****         All rights reserved        ****
; ********************************************

; This file can be changed manually with a text editor. No errors will be
; displayed by VEGA loading the configuration. All fields are case-insensitive.


; **** General preferences ****
;
; Language:
; (ignored by AmigaOS)

LANGUAGE        Auto

; Default output format:

OUTFORMAT	PDB2

; Overlapping tolerance for connecctivity calculation (%)

CONNTOL         20.0

; Starting residue for renumbering:

RENSTART	1

; **** Interaction energy calculation ****
;
; Contact distance for score calculation 

ENERGY_CONTDIST 2.5

; Cutoff distance (Amstrong):

ENERGY_CUTOFF	10.0

; Filter for energy decopmosition by residue (%):

ENERGY_FILTER	1.0

; Dielectric constant:

ENERGY_DIEL	1

; **** Info format ****
;
; Max atom number for calculation of extra information:
; Surface, volume, logP, etc.

MAXATMINFO      5000

; **** Mopac format ****
;
; Default keywords:

MOPAC_DEF	AM1 PRECISE GEO-OK

; Charge calculation (AUTO/charge):

MOPAC_CRG	AUTO

; Peptide bond correction (AUTO/ON/OFF):

MOPAC_MMOK	AUTO

; **** SAS parameters ****
;
; Probe radius (A):

SAS_PROBERAD	1.4

; Dot density:

SAS_POINTS	10

; **** Shell generation ****
;
; Box length / Sphere radius / Shell (A):

SOL_RADIUS	10.0

; Shape type (Box, Sphere, Shell):

SOL_SHAPE	BOX

; **** Volume calculation ****
;
; Dot density for cubic Angstrom

VOL_DENSITY     12

; **** HyperDrive parameters ****
;
; Number of CPUs used by HyperDrive (0 = all installed CPUs)

MAXCPU              0

; **** OpenCL ****
;
; Device type:
; None = OpenCL disabled
; Auto = Automatic detection
; Default = default device
; Accelerator = generic accelerator (e.g. IBM Cell Broadband Engine)
; CPU = generic CPU with SSE3 support (specific driver required)
; GPU = Graphic Processing Unit
;
; For the CPU device, a specific driver must be installed (e.g. included in the
; AMD Stream package).

OCLDEVTYPE         Auto

; **** XTC compression ****
;
; Number of digits after the point (from 1 to 8)

XTCPREC 3

APPENDIX C - CVFF atom types

The CVFF.tem file is stored in Data directory.

#TemplateFF CVFF 3.0

; ******************************
; ****  VEGA Template V4.0  ****
; ****   Force Field CVFF   ****
; ******************************


; ATDL atom description:
; ~~~~~~~~~~~~~~~~~~~~~~
; Element (2) - Bond order (1) - Ring indicator (1) - Aromatic indicator (1)
;
; The brackets indicates the length in characters of each field.

; Generic elements:                     Bond order:
; ~~~~~~~~~~~~~~~~~                     ~~~~~~~~~~~
; X = Any atom                          0   = Atom not bonded
; # = Heavy atom                        1-6 = Bond order
; $ = Any atom excluding C and H        9   = Any bond order
; @ = Halogen
; - = None

; Ring indicator:                       Aromatic indicator:
; ~~~~~~~~~~~~~~~                       ~~~~~~~~~~~~~~~~~~~
; 0     = Don't check ring              0 = Don't check
; 2     = Not inside a ring             1 = Aromatic
; 3...7 = From 3 to 7 member ring
; 9     = Generic ring

; Logical operators:
; ~~~~~~~~~~~~~~~~~~
; to use the logical operators AND, OR and NOT (&, | and !), you must
; place the expression between square brackets at the specified position:
;
; Examples:
; [C- |  N-]900  -> the element can be carbon or nitrogen
; [X- & !Cl]900  -> all elements but not chlorine
; C-[4 | 3]00    -> sp3 or sp2 carbon
; C-4[9 & 9]0    -> sp3 carbon in a double condensed ring
; C-3[6 | 5][!1] -> sp2 carbon in 5 or 6 member ring not aromatic

; Atom types:
; ~~~~~~~~~~~
; each not blank and not commented line (; is the remark indicator) must
; include at least the atom type name (max. 8 characters) and the ATDL
; description. Optionally, you can specify the bonded atoms placing them
; between round brackets.


; Type    Atm    Bonded atoms
; ========================================================================; ATDL atom description:
; ~~~~~~~~~~~~~~~~~~~~~~
; Element (2) - Bond order (1) - Ring indicator (1) - Aromatic indicator (1)
;
; The brackets indicates the length in characters of each field.

; Generic elements:                     Bond order:
; ~~~~~~~~~~~~~~~~~                     ~~~~~~~~~~~
; X = Any atom                          0   = Atom not bonded
; # = Heavy atom                        1-6 = Bond order
; $ = Any atom excluding C and H        9   = Any bond order
; @ = Halogen
; - = None

; Ring indicator:                       Aromatic indicator:
; ~~~~~~~~~~~~~~~                       ~~~~~~~~~~~~~~~~~~~
; 0     = Don't check ring              0 = Don't check
; 2     = Not inside a ring             1 = Aromatic
; 3...7 = From 3 to 7 member ring
; 9     = Generic ring

; Logical operators:
; ~~~~~~~~~~~~~~~~~~
; to use the logical operators AND, OR and NOT (&, | and !), you must
; place the expression between square brackets at the specified position:
;
; Examples:
; [C- |  N-]900  -> the element can be carbon or nitrogen
; [X- & !Cl]900  -> all elements but not chlorine
; C-[4 | 3]00    -> sp3 or sp2 carbon
; C-4[9 & 9]0    -> sp3 carbon in a double condensed ring
; C-3[6 | 5][!1] -> sp2 carbon in 5 or 6 member ring not aromatic

; Atom types:
; ~~~~~~~~~~~
; each not blank and not commented line (; is the remark indicator) must
; include at least the atom type name (max. 8 characters) and the ATDL
; description. Optionally, you can specify the bonded atoms placing them
; between round brackets.


; Type    Atm    Bonded atoms
; ========================================================================

  h    H-100  (C-900)
  h+   H-100  (N-400)
  hn   H-100  (N-900)
  h*   H-100  (O-200 (H-100 H-100))
  ho   H-100  (O-900)
  hp   H-100  (P-900)
  hs   H-100  (S-900)
  dw   D-100  (O-200 (D-100 H-100))
  dw   D-100  (O-200 (D-100 D-100))
  d    D-100  (X-900)

  c3h  C-430  (C-430 H-100 H-100 #-930)
  c3m  C-430  (C-430 #-930 X-900 X-900)
  c4h  C-440  (H-100 H-100 X-940 X-940)
  c4m  C-440  (X-940 X-940 X-900 X-900)
  cg   C-400  (N-400 (H-100 H-100) C-300 H-100 H-100)
  cg   C-400  (N-300 (H-100) C-300 H-100 H-100)
  ca   C-400  (N-400 C-300 H-100 X-900)
  ca   C-400  (N-300 C-300 H-100 X-900)
  coh  C-400  (O-200 (C-900) O-200 H-100 X-900)
  co   C-400  (O-200 (C-900) O-200 X-900 X-900)
  c3   C-400  (H-100 H-100 H-100 X-900)
  c2   C-400  (H-100 H-100 #-900 #-900)
  c1   C-400  (H-100 #-900 #-900 #-900)
  cn   C-400  (N-400 X-900 X-900 X-900)
  cn   C-400  (N-300 X-900 X-900 X-900)
  c    C-400  (X-900 X-900 X-900 X-900)
  ci   C-351  (N-351 (H-100) N-351 (H-100) X-900)
  cs   C-351  (S-251 X-951 X-900)
  c5   C-351  (X-951 X-951 X-900)
  cp   C-391  (X-991 X-991 X-900)
  cr   C-300  (N-300 N-300 N-300)
  cr   C-300  (N-200 N-300 N-300)
  c'   C-300  (O-100 N-300 X-900)
  c-   C-300  (O-100 O-100 X-900)
  c"   C-300  (O-100 X-900 X-900)
  c=   C-300  (X-900 X-900 X-900)
  ct   C-200  (X-900 X-900)

  n4   N-400  (X-900 X-900 X-900 X-900)
  ni   N-351  (C-351 (N-351) C-351 H-100)
  np   N-391  (X-991 X-991)
  no   N-300  (O-100 O-100)
  n1   N-300  (C-300 (N-300 N-300) C-400 H-100)
  n2   N-300  (C-300 (N-300 N-900) H-100 H-100)
  n    N-300  (C-300 (O-100) X-900 X-900)
  n3   N-300  (X-900 X-900 X-900)
  np   N-291  (X-991 X-991)
  n=   N-200  (X-900 X-900)
  nt   N-100  (X-900)

  o*   O-200  (H-100 H-100)
  oh   O-200  (H-100 X-900)
  o-   O-200  (Mg900 C-900)
  o-   O-200  (Zn900 C-900)
  o    O-200  (X-900 X-900)
  o-   O-300  (Mg900 Mg900 C-900)
  o-   O-100  (C-300 (O-100 O-100))
  o-   O-100  (P-400)
  o'   O-100  (C-300)
  o'   O-100  (N-300 (O-100 O-100))
  o'   O-100  (S-400)
  oo   O-900  (O-900 Fe900)

  s    S-400
  sh   S-200  (H-100 C-900)
  s    S-200  (C-900 X-900)
  s1   S-200  (S-200 X-900)
  s    S-100

  p    P-900
  si   Si900

  f    F-100  (C-900)
  cl   Cl100  (C-900)
  Cl   Cl000
  br   Br100  (C-900)
  Br   Br000
  i    I-900

  ar   Ar000
  Na   Na000
  c+   Ca000
  c+   Mg900
  cu   Cu900
  fe   Fe900
  pt   Pt900
  Zn   Zn900

  nu   Nu900

APPENDIX C - TRIPOS atom types

The TRIPOS.tem file is stored in Data directory and it contains the new atom types with more than four character length.

#TemplateFF TRIPOS 3.1

; ******************************
; ****  VEGA Template V4.0  ****
; ****  Force Field TRIPOS  ****
; ******************************


; ATDL atom description:
; ~~~~~~~~~~~~~~~~~~~~~~
; Element (2) - Bond order (1) - Ring indicator (1) - Aromatic indicator (1)
;
; The brackets indicates the length in characters of each field.

; Generic elements:                     Bond order:
; ~~~~~~~~~~~~~~~~~                     ~~~~~~~~~~~
; X = Any atom                          0   = Atom not bonded
; # = Heavy atom                        1-6 = Bond order
; $ = Any atom excluding C and H        9   = Any bond order
; @ = Halogen
; - = None

; Ring indicator:                       Aromatic indicator:
; ~~~~~~~~~~~~~~~                       ~~~~~~~~~~~~~~~~~~~
; 0     = Don't check ring              0 = Don't check
; 2     = Not inside a ring             1 = Aromatic
; 3...7 = From 3 to 7 member ring
; 9     = Generic ring

; Logical operators:
; ~~~~~~~~~~~~~~~~~~
; to use the logical operators AND, OR and NOT (&, | and !), you must
; place the expression between square brackets at the specified position:
;
; Examples:
; [C- |  N-]900  -> the element can be carbon or nitrogen
; [X- & !Cl]900  -> all elements but not chlorine
; C-[4 | 3]00    -> sp3 or sp2 carbon
; C-4[9 & 9]0    -> sp3 carbon in a double condensed ring
; C-3[6 | 5][!1] -> sp2 carbon in 5 or 6 member ring not aromatic

; Atom types:
; ~~~~~~~~~~~
; each not blank and not commented line (; is the remark indicator) must
; include at least the atom type name (max. 8 characters) and the ATDL
; description. Optionally, you can specify the bonded atoms placing them
; between round brackets.


; Type    Atm    Bonded atoms
; ========================================================================

  H.t3p  H-100 (O-200 (H-100 H-100))
; H.spc  H-100 (O-200 (H-100 H-100))
  H      H-100

  C.3    C-400
  C.ar   C-391
  C.cat  C-300 (N-300 N-300 N-300)
  C.2    C-300
  C.1    C-200

  N.4    N-400
  N.ar   N-391
  N.am   N-300 (C-300 (O-100))
  N.pl3  N-300 (C-300)
  N.3    N-300
  N.ar   N-291
  N.2    N-200
  N.1    N-100

  O.t3p  O-200 (H-100 H-100)
; O.spc  O-200 (H-100 H-100)
  O.3    O-200
  O.ar   O-291
  O.co2  O-100 (C-300 (O-100 O-100))
  O.co2  O-100 (P-400 (O-100 O-100 O-100))
  O.2    O-100

  S.3    S-400 (Lp100 Lp100)
  S.O2   S-400 (O-100 O-100)
  S.O    S-300 (O-100)
  S.3    S-200
; S.ar   S-291
  S.2    S-100

  P.3    P-400

  I      I-100
  I      I-000
  F      F-100
  F      F-000
  Cl     Cl100
  Cl     Cl000
  Br     Br100
  Br     Br000

  Se     Se900
  Si     Si400

  Na     Na900
  K      K-900
  Ca     Ca900
  Mg     Mg900
  Li     Li900
  Al     Al900
  Fe     Fe900
  Mn     Mn900
  Mo     Mo900
  Co.oh  Co900
  Cr.th  Cr300
  Cr.oh  Cr600
  Zn     Zn900
  Sn     Sn900

  Du     Du900
  LP     Lp900

  Hev    #-900
  Any    X-900

APPENDIX C - UNIV atom types

The UNIV.tem file is stored in Data directory.

#TemplateFF UNIV 1.0

; ******************************
; ****  VEGA Template V3.0  ****
; ****   UNIV atom types    ****
; ******************************


; NOTE:
; This template is expecially designed for Gasteiger-Marsili charge template and
; can't be renamed or removed. It's based on MENG atom type definitions.

; Description:
; ~~~~~~~~~~~~
; Generic atom type - Bond order - Ring indicator - Aromatic indicator

; Generic atom types:                   Bond order:
; ~~~~~~~~~~~~~~~~~~~                   ~~~~~~~~~~~
; X = Any atom                          0   = Atom not bonded
; # = Heavy atom                        1-6 = Bond order
; $ = Any atom excluding C and H        9   = Any bond order
; @ = Halogen
; - = None

; Ring Indicator:                       Aromatic Indicator:
; ~~~~~~~~~~~~~~~                       ~~~~~~~~~~~~~~~~~~~
; 0     = Don't check ring              0 = Don't check
; 3...6 = From 3 to 6 member ring       1 = Aromatic
; 9     = Generic ring


; Type Atm    Bonded Atoms
; ========================================================================
  HOS3 H-100 (O-200 (S-400))
  H    H-100

  CSO2 C-400 (S-400 (O-100 O-100 N-900 C-900))
  CSO2 C-400 (S-400 (O-100 O-100 C-900 C-900))
  C3   C-400
  CSO2 C-300 (S-400 (O-100 O-100 N-300 C-900))
  CSO2 C-300 (S-400 (O-100 O-100 C-900 C-900))
  CS2  C-300 (S-100 C-900 C-900)
  CG   C-300 (N-300 N-300 N-300)
  C2   C-300
  C1   C-200
  CN   C-100 (N-100)

  N3+  N-400
  N3   N-361 (C-361 (O-100) C-361)
  NP+  N-361
  NI+  N-351 (C-351 (N-351 N-351))
  NG   N-300 (C-300 (N-300 N-300 N-300))
  NSO2 N-300 (S-400 (O-100 O-100 N-300 C-900))
  N3   N-300
  N2   N-200
  NC   N-100 (C-100)
  N1   N-100

  O3   O-200  (P-400 P-400)
  O3   O-200  (P-400 C-900)
  OP   O-200  (P-400 (O-200 O-200 O-100 O-100))
  OS4E O-200  (S-400 (O-100 O-100 O-200 O-900))
  OS1  O-200  (S-400 H-100)
  O-   O-200  (C-300 Zn900)
  O3   O-200
  
  O3   O-100  (S-400 (O-100 O-100 O-200 (C-900) C-900))
  OS4  O-100  (S-400 (O-100 O-100 O-100 O-900))
  OS3  O-100  (S-400 (O-100 O-100 O-100 C-900))
  OS2  O-100  (S-400 (O-100 O-100 C-900 C-900))
  OS2  O-100  (S-400 (O-100 O-100 N-300 C-900))
  OS1  O-100  (S-400)
  OS1  O-100  (S-300)
  O-   O-100  (C-300 (O-100 O-100))
  OP   O-100  (P-400 (O-200 O-200 O-100 O-100))
  OP   O-100  (P-400 (O-200 N-300 O-100 O-100))
  OP=  O-100  (P-400 (O-100 O-100 O-100))
  O2   O-100

  SO4  S-400  (O-100 O-100 O-900 O-900)
  SO3H S-400  (O-200 (H-100) O-100 O-100)
  SO3- S-400  (O-100 O-100 O-100 C-900)
  SO2  S-400  (O-100 O-100 C-900 #-900)
  SO1  S-300  (O-100 C-900 C-900)
  S+   S-300
  S-   S-200  (C-400 Zn900)
  S3   S-200
  S-   S-100  (C-400)
  S-   S-100  (C-350 (N-250 S-250))
  S2   S-100  (C-300)
  S2   S-100  (C-200)
  PN   P-400  (O-200 O-200 O-100 O-100)
  P=   P-400  (O-100 O-100 O-100)
  P    P-900

  F0   F-000
  Cl0  Cl000
  Br0  Br000
  I0   I-000

  F    F-900
  Cl   Cl900
  Br   Br900
  I    I-900

  Na   Na900
  K    K-900
  Ca   Ca900
  Mg   Mg900
  Mn   Mn900
  Co   Co900
  Cr3+ Cr000
  Fe   Fe900
  Zn   Zn900

  Du   X-900

APPENDIX D –  CSV Surface Format

The CSV Surface Format is a simple Comma Separated Values (CSV) file in which the field separator is the semicolon character (;) and uses the following format:

12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789
NNNNNN; XXXXXX.XXXXXXXX; YYYYYY.YYYYYYYY; ZZZZZZ.ZZZZZZZZ; VVVVVV.VVVVVVVV; RRR; GGG; BBB

NNNNNN          <- Number of the atom associated to the surface dot (C: %6d, Fortran: i6)
XXXXXX.XXXXXXXX <- X coordinate (C: %15.8f, Fortran: f15.8)
YYYYYY.YYYYYYYY <- Y coordinate (C: %15.8f, Fortran: f15.8)
ZZZZZZ.ZZZZZZZZ <- Z coordinate (C: %15.8f, Fortran: f15.8)
VVVVVV.VVVVVVVV <- Property value projected to the surface dot  (C: %15.8f, Fortran: f15.8)
RRR             <- Red component of the dot color (C: %3d, Fortran: i3)
GGG             <- Green component of the dot color (C: %3d, Fortran: i3)
BBB             <- Blue component of the dot color (C: %3d, Fortran: i3)

Example:

...
    19;      6.75958252;      1.91035986;      1.95385861;      0.00207091;   0;   0; 255
    19;      7.02752399;      2.00558615;      1.95385861;     -0.00113359;  47; 255;   0
    19;      7.08981323;      4.05955124;      1.76369834;      0.00192202;  87; 255;   0
    19;      6.82545519;      4.15205383;      1.76369834;      0.00394259; 113; 255;   0
    19;      6.82545519;      1.71330953;      1.76369834;     -0.00801759;   0; 255;  42
    19;      6.82479095;      4.32851887;      1.54213154;     -0.00837863;   0; 255;  47
    19;      6.54714155;      4.35586500;      1.54213154;     -0.00651778;   0; 255;  23
    19;      6.26949215;      4.32851887;      1.54213154;     -0.00380767;  12; 255;   0
    19;      6.00251293;      4.24753141;      1.54213154;     -0.00061359;  53; 255;   0
    19;      5.75646353;      4.11601543;      1.54213154;      0.00250929;  94; 255;   0
...
    48;      6.40636539;      3.02671599;      2.81072426;      0.03325002; 255;  12;   0
    48;      6.60387897;      3.02671599;      2.79435802;      0.03198734; 255;  29;   0
    48;      6.50512218;      3.19776773;      2.79435802;      0.03299629; 255;  15;   0
    48;      6.30760860;      3.19776773;      2.79435802;      0.03386965; 255;   4;   0
    48;      6.20885181;      3.02671599;      2.79435802;      0.03395212; 255;   3;   0
    48;      6.30760860;      2.85566425;      2.79435802;      0.03302151; 255;  15;   0
    48;      6.50512218;      2.85566425;      2.79435802;      0.03195009; 255;  29;   0
    48;      6.79600477;      3.02671599;      2.74570513;      0.03010002; 255;  53;   0
    48;      6.74380302;      3.22153568;      2.74570513;      0.03116508; 255;  39;   0
    48;      6.60118484;      3.36415362;      2.74570513;      0.03226105; 255;  25;   0
...

APPENDIX D –  DATABASE FORMATS

IUPAC database

The IUPAC database (.iup or .txt) is a text file in which each line includes the IUPAC name of each molecule.

File format example:

Bis(2-naphthyl)methane
dinaphthalen-2-ylmethane
2-(naphthalen-2-ylmethyl)naphthalene
4H-benzo[d][1,3]dithiine
3,6,8-trioxabicyclo[3.2.2]nonane
2(10),3-Pinadiene
Perfluoro(1-methylperhydronaphthalene)
4-(Isopropylidenehydrazono)-2,5-cyclohexadiene-1-carboxylic acid
1-Ethylidene-5-(2-naphthyl)carbonohydrazide

SMILES database

The SMILES database (.smi or .txt) is a text file in which each line includes two fields (the SMILES string and the molecule name) separated by one or more spaces or tabs. If the molecule name contains spaces, it must be quoted by using double quotes.

File format example:

CC(=O)Oc1ccccc1C(O)=O "Aspirin (ASA)"
CC1=CN(C2CC(N=NN)C(CO)O2)C(=O)NC1=O AZT
CN1C(=O)c2c([n]c[n]2C)N(C)C1=O Caffeine
[NH3+][Pt]([NH3+])(Cl)Cl Cisplantin
Nc1ccc(cc1)S(=O)(=O)c1ccc(N)cc1 Dapsone
CN1C(=O)CN=C(c2cc(Cl)ccc12)c1ccccc1 Diazepam
CNCC(O)c1cc(O)c(O)cc1 Epinefrine
CC12CCC3C(CCc4cc(O)ccc43)C1CCC2O Estradiol
CC(C)Cc1ccc(cc1)C(C)C(O)=O Ibuprofen
CN(C)CCCN1c2ccccc2CCc2ccccc12 Imipramine
CN1CCCC1c1c[n]ccc1 Nicotine
CN(C)CC1CCC(CSCCNC(=C[n](:o):o)NC)O1 Ranitidine
CC1OC(OC2C([nH]:c(:[nH2]):[nH2])C(O)C([nH]:c(:[nH2]):[nH2])C(O)C2O)C(OC2OC(CO)C(O)C(O)C2NC)C1(O)C=O Streptomycin

APPENDIX D - Interchange File Format (IFF) 1.4

The Interchange File Format (IFF) is a binary file with an AmigaOS chunk structure (like IFF-ILBM, AIFF, etc). All chunks are optional (with the exception of the first one) and the structure is totally expandable. Use this powerful format if you want store the largest number of information when you are using VEGA and VEGA ZZ.

Conventions for numeric formats:

IFF files are in big endian format and so if the hardware doesn’t support it (e.g. x86 CPUs), you must change the byte order when write the floats and integers which size is more than one character.
RIFF files (Resource Interchange File Format) are equivalent to IFF, but the numeric data is stored in little endian format and they are supported starting from VEGA ZZ 2.0.6 and VEGA 1.5.6.
A chunk is a data block with a 8 byte header:

Chunk {
    HEADER (8 bytes)
    Data
    ...
}

The first 4 bytes are a string identifying the chunk type and the next 4 bytes (ULONG format) are the size of Data block, as shown in the following C structure:

typedef struct {
    UBYTE  Hdr[4]
    ULONG  Size
} HEADER;

IFF file structure:

IFF_File {
    HEADER {
        "FORM",
        4 + sizeof(Chunk_1) + sizeof(Chunk_1) + ... + sizeof(Chunk_N)
    }
    "MOLE"

    Chunk_1
    Chunk_2
    ...
    Chunk_N

}

All IFF files are a sequence of chunks with a header of 8 bytes. The recognition string (Hdr field) is FORM and the Size field is the sum of lengths of all chunks and the size of subformat recognition header (8 bytes). IFF is a family of binary files that can store a variety of data as audio, image, video and molecule. To recognize the subformat you must read the next 8 byte containing the subformat header. In particular, this second header contains the sub-recognition string MOLE and the Size field with the value of the size of all data chunks.
If the file is in little endian format, the main chunk starts with RIFF string instead of FORM.

ATOM  -  Atom name chunk:

ATOM {
    HEADER {
        "ATOM",
        4 + 2 * TotAtm
    }
    ULONG  TotAtm
    UBYTE  Element[2][TotAtm]
}

This is the only one chunk that can't be optional. TotAtm is the total number of atoms stored in the file. Element is a two byte vector containing the names of chemical elements for each atom. If the element name has the size of one character (e.g. H, C, O, S, etc), the second byte must be a space. The special Xc element name is reserved for centroids (dummy atoms). For example,  the ATOM chunk of chlorobenzene (C₆H₅Cl, 12 atoms) must be:

ATOM {
    HEADER {
        "ATOM",
        24,
    }
    "C ", "C ", "C ", "C ", "C ",
    "H ", "H ", "H ", "H ", "Cl"
}

XYZ1  -  Single precision Cartesian coordinate chunk:

XYZ1 {
    HEADER {
        "XYZ1",
        TotAtm * 12
    }
    XYZ[TotAtm] {
        FLOAT  x
        FLOAT  y
        FLOAT  z
    }
}

This chunk contains the Cartesian coordinates for each atom in single precision floating-point format. This chunk and the XYZ2 could be repeated more thane one time if the file is a MD trajectory. For example, the XYZ1 chunk of benzene (C₆H₆) could be:

XYZ1 {
    HEADER {
        "XYZ1",
        144
    }
    XYZ {
        { 0.695,  1.203,  0.000 },
        {-0.695,  1.203, -0.002 },
        {-1.389,  0.000, -0.006 },
        {-0.695, -1.203, -0.007 },
        { 0.695, -1.203, -0.006 },
        { 1.389,  0.000, -0.002 },
        { 1.235,  2.139,  0.003 },
        {-1.235,  2.139, -0.001 },
        {-2.470,  0.000, -0.007 },
        {-1.235, -2.139, -0.010 },
        { 1.235, -2.139, -0.007 },
        { 2.470,  0.000, -0.001 }
    }
}

XYZ2  -  Double precision Cartesian coordinate chunk:

XYZ2 {
    HEADER {
        "XYZ1",
        TotAtm * 24
    }
    XYZ[TotAtm] {
        DOUBLE  x
        DOUBLE  y
        DOUBLE  z
    }
}

XYZ2 is the double precision version of XYZ1 chunk, keeping the same structure.

CENT  -  Centroid chunk:

CENT {
    HEADER {
        "CENT",
        4 + 5 * TotCent + TotRefAtm * 4
    }
    ULONG TotCent;
    CENTROIDS[TotCent] {
        ULONG  CentID
        BYTE   TotRef
        ULONG  RefAtmID[TotRef]
    }
}

Centroids are dummy atoms labelled as Xc in the element chunk (ATOM). This chunk contains the data to calculate dynamically the position of each centroid. TotCent is the number of centroids, CentID is the identification number of the centroid (it's the normal atom serial number), TotRef is the number of the atoms used to calculate dynamically the centroid position, RefAtmID is the array containing the serials of the atoms used to calculate the position. TotRefAtm in the IFF header is the number of all atoms involved in the position calculation of all centroids. If this chunk is missing, the centroids specified in the ATOM chunk will be considered fixed and their coordinates aren't dynamically calculated when the coordinates of the reference atoms are changed.

CHIR  -  Chirality chunk:

VGCL {
    HEADER {
        "CHIR",
        TotAtm
    }
    BYTE  Chiral[TotAtm]
}

It stores the chirality flag of each atom. The possible values of each array elements are:

CONX  -  Connectivity chunk:

CONX {
    HEADER {
        "CONX",
        TotBond * 9
    }
    ULONG TotBond;
    CONN[TotBond] {
        ULONG  Atom1
        ULONG  Atom2
        UBYTE  BondOrder
    }
}

This chunk is needed to indicate the connectivity between atom pairs. TotBond is the number of bonds, Atom1 and Atom2 is the pair of connected atom and BondOrder is the bond order that can be 1 (single bond), 2 (double bond), 3 (triple bond) and 4 (partial double bond).

IIUB  -  IUPAC IUB atom name chunk:

IIUB {
    HEADER {
        "IIUB",
        TotAtm * IUB_Len
    }
    UBYTE  IUB_Len
    UBYTE  Name[IUB_Len][TotAtm]
}

In this chunk you can find the IUPAC IUB atom names. IUB_Len is the length of Name record.

CALC  -  Potential and atomic charges chunk:

CALC {
    HEADER {
        "CALC",
        18 + sizeof(ForceFieldName[ ]) + TotAtm * (4 + ATPY_Len)
    }
    UBYTE  ForceFieldName[ ]
    HEADER {
        "CHRG",
        TotAtm * 4
    }
    FLOAT  AtmCharge[TotAtm]

    HEADER {
        "ATYP",
        TotAtm * ATPY_Len
    }
    UBYTE  ATPY_Len
    UBYTE  AtmType[ATPY_Len][TotAtm]
}

This is a complex chunk containing the atom type and the atomic charge of each atom. In this chunk, two sub-chunk are present: CHRG and ATYP. The former includes the atomic charges in single precision format (AtmCharge) and the latter stores the atom potentials (atom types). ATPY_Len is the size (in bytes) of each potential record. At this time, the default value is 8.

FIXA  -  Atom constraints chunk:

FIXA {
    HEADER {
        "FIXA",
        TotAtm
    }
    FLOAT  FixValue[TotAtm]
}

This chunk contains constraint values used by molecular dynamics simulations. Each value is a positive floating point number, usually ranged from 0 (free) to 1 (fix).

RESI  -  Residue name, residue number and chain identification chunk:

RESI {
    HEADER {
        "RESI",
        TotRes * 13
    }
    RESDATA[TotRes] {
        ULONG  Atoms
        UBYTE  ResName[4]
        UBYTE  ResNum[4]
        UBYTE  ChainID
    }
}

TotRes is the total number of residues, Atoms is the number of atoms in the residue, ResName is the residue name, ResNum is the residue number and ChainID is the chain indicator. ChainID contains the chain identification character or a null value.

RSNU  -  Residue number chunk (obsolete):

RSNU {
    HEADER {
        "RSNU",
        TotAtm * 4
    }
    UBYTE  ResNum[4][TotAtm]
}

It's the residue number of each atom. ResNum is a four character string and not an integer number, because it can include the chain indicator (e.g. "99 A"). This chunk was maintained for backward compatibility only and  it was replaced by RESI chunk.

RSNA  -  Residue name chunk (obsolete):

RSNA {
    HEADER {
        "RSNA",
        TotRes * 4
    }
    UWORD  TotRes
    RESNAME[TotRes] {
        UBYTE  ResNum[4]
        UBYTE  ResName[4]
    }
}

This chunk is used to translate the residue number ResNum to residue name ResName. TotRes is the total number of residue in the file. This chunk was maintained for backward compatibility only and  it was replaced by RESI chunk.

SEGM  -  Segments chunk:

SEGM {
    HEADER {
        "SEGM",
        TotSeg * 4
    }
    ULONG  AtmNum[TotSeg]
}

This chunk is equivalent to TER record in PDB file format. TotSeg is the number of segments and AtmNum is a vector containing the atom IDs (progressive number) indicating the end of each segment.

MOLM  -  Name of the molecules chunk:

MOLM {
    HEADER {
        "MOLM",
        sizeof(MOLNAME[ ])
    }
    ULONG  TotMol
    MOLNAME[TotMol] {
        ULONG  AtmStart
        ULONG  AtmNum
        UBYTE  MolName[ ]
    }
}

IFF files can include more than one molecule. TotMol is the total number of molecules, AtmStart is the first atom number of the molecule, AtmNum is the number of atoms in the selected molecule and MolName is the molecule name (C string format, null terminated).

MOLN  -  Name of the molecules chunk:

MOLN {
    HEADER {
        "MOLN",
        sizeof(MOLNAME[ ])
    }
    UWORD  TotMol
    MOLNAME[TotMol] {
        ULONG  AtmStart
        ULONG  AtmNum
        UBYTE  MolName[ ]
    }
}

This chunk is replaced by MOLM and it's kept for compatibility.

COMM  -  Remark chunk:

COMM {
    HEADER {
        "COMM",
        1 + sizeof(Remark[ ])
    }
    UBYTE  Remark[ ]
}

In this chunk, you can include a remark.

SRFA  -  Surface atom number chunk:

SRFA {
    HEADER {
        "SRFA",
        Points * 4
    }
    ULONG  AtmNum[Points]
}

It stores the atom number for each surface point. This chunk requires the SURF chunk before it.

SRC3  -  Surface color chunk (24 bit):

SRC3 {
    HEADER {
        "SRC3",
        Points * 3
    }
    DOTCOLOR[Points] {
      UBYTE  R
      UBYTE  G
      UBYTE  B
    }
}

This chunk contains the color for each surface point in RGB format (24 bit), where R is the red component , G is the green component and B is the blue component. All these parameters must be in the range from 0 to 255. This is the default color chunk written by VEGA ZZ. You can use SRFC chunk also, preferring SRC3 if the alpha (transparency) information isn't required.

SRFC  -  Surface color chunk (32 bit):

SRFC {
    HEADER {
        "SRFC",
        Points * 4
    }
    DOTCOLOR[Points] {
      UBYTE  A
      UBYTE  R
      UBYTE  G
      UBYTE  B
    }
}

This chunk contains the color for each surface point in ARGB format, where A is the alpha key (transparency), R is the red component , G is the green component and B is the blue component. All these parameters must be in the range from 0 to 255.

SRFF  -  Surface face chunk:

SRFF {
    HEADER {
        "SRFF",
        NumVertexID * Size + 1
    }
    UBYTE  Size
    UBYTE  (or UWORD, or ULONG) VertexIDArray[NumVertexID]
}

This chunk contains the surface faces as triplets of vertex IDs. The vertex ID is a positive integer number indicating the surface dot (see SURF chunk) used to define one face (triangle) vertex. The vertex IDs can be stored in the formats defined by the Size byte: UBYTE (Size = 1), UWORD (Size = 2) and ULONG (Size = 3). The three formats are able to store respectively until 256, 65536 and 4294967296 vertex IDs.

SRFV  -  Surface value chunk:

SRFV {
    HEADER {
        "SRFV",
        Points * 4
    }
    FLOAT  Value[Points]
}

It contains the property value of each surface dot.

SRFI  -  Surface information chunk:

SRFI {
    HEADER {
        "SRFI",
        LenOfSrfName + 16
    }
    UBYTE  LenOfSrfName
    UBYTE  SrfName[LenOfSrfName]
    LONG   Flags
    UBYTE  SrfType
    UBYTE  Alpha
    UBYTE  DotSize
    ULONG  Reserved1
    ULONG  Reserved2
}

If you want to add extra information to surfaces, you can use this chunk in which SrfName is the surface name, LenOfSrfName is the length of the surface name (max. 255 characters),  Flags is the special surface flags (click here for more information), SrfType is the surface type (click here for more information), Alpha is the alpha blending value (0 full transparent, 255 full opaque) and DotSize is the dot size used to show the dotted surface. LenOfSrfName can be zero, but in this case SrfName mustn't present in the chunk. Reserved1 and Reserved2 are for future use.

SRFN  -  Surface normal chunk:

SRFN {
    HEADER {
        "SRFN",
        Points * 6 
    }
    XYZ[Points] {
        WORD  x
        WORD  y
        WORD  z
    }
}

This chunk stores the normal vectors of each surface point used by VEGA ZZ lighting engine for shading. If the surface type is dotted, this chunk is ignored. The normals, which values are in range from -1.0 to 1.0, are stored in low precision integer format. When you want put the normals in the chunk, you must multiply each coordinate by 32767 and thus you must take the integer part. To revert the floating point format, you must divide the coordinates by 32767 and cast to float. In this way, you can obtain a good precision using half of disk space.  

SURF  -  Generic surface chunk:

SURF {
    HEADER {
        "SURF",
        Points * 12
    }
    XYZ[Points] {
        FLOAT  x
        FLOAT  y
        FLOAT  z
    }
}

This chunk contains the Cartesian coordinates of each surface point. Points is the number of surface points. The IFF format allows more than one surfaces and so one or more SURF chunk can be present in the file. Please remember that this chunk must written before all other surfaces chunk otherwise they will be ignored. All other surface chunk are optional.

VERS  -  Version chunk:

The chunk contains the file version number organized in two 16 bit words: the higher word is the version and the lower word is the revision.

Special VEGA chunks:

VGAB  -  Active atom chunk:

VGAB {
    HEADER {
        "VGAB",
        (TotAtm / 8) + 1
    }
    UBYTE  Active[(TotAtm / 8) + 1]
}

It defines if the atom is active or not (visible or not). The boolean values are stored in a bitmap in order to reduce the size and so this chunk is eight time smaller then the previous VGAC. If a bit is true (1), the atom is active, otherwise if it's false (0), the atom is inactive. To encode/decode this chunk, you can use the routines at the end of this document.

VGAC  -  Active atom chunk (obsolete):

VGAC {
    HEADER {
        "VGAC",
        TotAtm
    }
    UBYTE  Active[TotAtm]
}

It defines if the atom is active or not (visible or not). If a vector item is true (1), the atom is active, otherwise if it's false (0), the atom is inactive. This chunk is obsolete and it's replaced by VGAB. 

VGCL  -  Color chunk:

VGCL {
    HEADER {
        "VGCL",
        TotAtm
    }
    UBYTE  ColorID[TotAtm]
}

It stores the color of each atom with the VEGA color code. See below for all color codes.

VGDM  -  Draw mode chunk:

VGDM {
    HEADER {
        "VGDM",
        TotAtm
    }
    UBYTE  DrawMode[TotAtm]
}

It stores the information about the draw mode of each atom. Starting from VEGA ZZ 2.0.0, it's possible to change the display mode of each atom. See below for the draw modes.

VGLB  -  Label chunk:

VGLB {
    HEADER {
        "VGLB",
        TotAtm
    }
    UBYTE  Label[TotAtm]
}

This chunk stores the label of each atom. See below for label codes.

VGMO  -  Monitor chunk:

VGLB {
    HEADER {
        "VGMO",
        The size can't be pre-computed
    }
    MONITOR[TotMon] {
        UBYTE  MonType
        IF (MonType != 0x10) {
            UBYTE  LblLen
            BYTE  Label[LblLen]
        IF (NonType == 0x20) {
            ULONG  AtmNum[2]
            BYTE   EzGeom
        } ELSE {
            ULONG  AtmNum[MonType & 0xf]
        }
    } 
}

This chunk contains the information for the monitors. The MonType byte is the monitor type as reported in the following table:

AtmNum is the vector of atom numbers defining the monitor and its size can be obtained by MonType AND (logical operator) 0xf (16). If MonType is 0x10, the AtmNum array is replaced by the LblLen unsigned byte and Label byte array containing the H-bond label. If MonType is 0x20, AtmNum array has two elements only and the EzGeom byte is added.

VGTR  -  Transformation chunk:

VGAC {
    HEADER {
        "VGTR",
        TotAtm
    }
    FLOAT  PosX
    FLOAT  PosY
    FLOAT  PosZ

    FLOAT  RotStepX
    FLOAT  RotStepY
    FLOAT  RotStepZ

    FLOAT  PosStepX
    FLOAT  PosStepY
    FLOAT  PosStepZ

    FLOAT  Scale

    FLOAT  RotMat[4][4]
}

This chunk is only for private use and stores the current view settings of VEGA ZZ.

C subroutines and definitions:

In order to simplify the C programming, some useful definitions and subroutines are reported:

/**** VEGA atom label definitions ****

#define VG_ATMLBL_NONE       0
#define VG_ATMLBL_NAME       1
#define VG_ATMLBL_ELEMENT    2
#define VG_ATMLBL_NUMBER     3
#define VG_ATMLBL_TYPE       4
#define VG_ATMLBL_CHARGE     5
#define VG_ATMLBL_CHIRAL     6
#define VG_ATMLBL_FIX        7
#define VG_ATMLBL_RESNAMESEQ 8
#define VG_ATMLBL_RESNAME    9
#define VG_ATMLBL_RESSEQ    10

/**** VEGA color definitions ****/

#define VGCOL_NONE           0
#define VGCOL_BLACK          1
#define VGCOL_WHITE          2
#define VGCOL_RED            3
#define VGCOL_GREEN          4
#define VGCOL_CYAN           5
#define VGCOL_YELLOW         6
#define VGCOL_FIREBIRCK      7
#define VGCOL_MAGENTA        8
#define VGCOL_PINK           9
#define VGCOL_VIOLET        10
#define VGCOL_GRAY          11
#define VGCOL_ORANGE        12
#define VGCOL_DARKGREEN     13
#define VGCOL_BLUE          14
#define VGCOL_DARKYELLOW    15
#define VGCOL_BROWN         16
#define VGCOL_SKYBLUE       17
#define VGCOL_DARKGRAY      18
#define VGCOL_GHOSTPINK     19
#define VGCOL_GHOSTGREEN    20
#define VGCOL_GHOSTBLUE     21
#define VGCOL_GHOSTYELLOW   22
#define VGCOL_GHOSTGRAY     23
#define VGCOL_SAND          24

/**** Draw modes ****/

#define VG_ATMD_WIREFRAME   0    /* Vectors only                */
#define VG_ATMD_CPK_DOTTED  1    /* CPK/Van der Waals dotted    */
#define VG_ATMD_CPK_WIRE    2    /* CPK/Van der Waals wireframe */
#define VG_ATMD_CPK_SOLID   3    /* CPK/Van der Waals solid     */
#define VG_ATMD_BALL_WIRE   4    /* Ball & stick wireframe      */
#define VG_ATMD_BALL_SOLID  5    /* Ball & stick solid          */
#define VG_ATMD_SICK_WIRE   7    /* Stick wireframe             */
#define VG_ATMD_SICK_SOLID  8    /* Stick solid                 */
#define VG_ATMD_TUBE_SOLID  8    /* Tube solid                  */
#define VG_ATMD_TRACE_SOLID 9    /* Trace solid                 */

#define VG_ATMC_NONE        0    /* Not chiral                  */
#define VG_ATMC_E         'E'    /* E geometry                  */
#define VG_ATMC_Z         'Z'    /* Z geometry                  */
#define VG_ATMC_R         'R'    /* R                           */
#define VG_ATMC_S         'S'    /* S                           */
#define VG_ATMC_UNDEF     '*'    /* Undefined chirality         */

/**** Surface Flags (see SRFI chunk) ****/

#define VG_SRFF_NONE        0    /* None                        */
#define VG_SRFF_ACTIVE      1    /* The surface is visible      */
#define VG_SRFF_ALPHA       2    /* Enable the alpha blending   */

/**** Surface types ****/

#define VG_SRFT_DOTTED      0    /* Dotted surface              */
#define VG_SRFT_MESH        1    /* Mesh surface                */
#define VG_SRFT_SOLID       2    /* Solid surface               */

/**** Types ****/

typedef char             BYTE;
typedef unsigned char    UBYTE;
typedef int              LONG;
typedef unsigned int     ULONG;
typedef short            WORD;
typedef unsigned short   UWORD;
typedef float            FLOAT;
typedef double           DOUBLE;

/**** IFF Chunk header ****/

typedef struct {
    char Hdr[4];
    ULONG Size;
} IFFHDR;

/**** Prototypes ****/

void SwapW(void *);
void SwapL(void *);
void SwapD(void *);


/**** Change the endian for WORD and UWORD ****/

void SwapW(register void *Val)
{
    register UBYTE T;
    T = ((UBYTE *)Val)[0];
    ((UBYTE *)Val)[0] = ((UBYTE *)Val)[1];
    ((UBYTE *)Val)[1] = T;
}


/**** Change endian for LONG, ULONG and FLOAT ****/

void SwapL(register void *Val)
{
    register UBYTE T;
    T = ((UBYTE *)Val)[0];
    ((UBYTE *)Val)[0] = ((UBYTE *)Val)[3];
    ((UBYTE *)Val)[3] = T;
    T = ((UBYTE *)Val)[1];
    ((UBYTE *)Val)[1] = ((UBYTE *)Val)[2];
    ((UBYTE *)Val)[2] = T;
}


/**** Change the endian for DOUBLE ****/

void SwapD(void *Val)
{
    register UBYTE T;
    T = ((UBYTE *)Val)[0];
    ((UBYTE *)Val)[0] = ((UBYTE *)Val)[7];
    ((UBYTE *)Val)[7] = T;
    T = ((UBYTE *)Val)[1];
    ((UBYTE *)Val)[1] = ((UBYTE *)Val)[6];
    ((UBYTE *)Val)[6] = T;
    T = ((UBYTE *)Val)[2];
    ((UBYTE *)Val)[2] = ((UBYTE *)Val)[5];
    ((UBYTE *)Val)[5] = T;
    T = ((UBYTE *)Val)[3];
    ((UBYTE *)Val)[3] = ((UBYTE *)Val)[4];
    ((UBYTE *)Val)[4] = T;
}


/**** Encode the active atom into the bitmap ****/

/*
 * Active -> An array of unsigned bytes from which the boolean values
 *           are packed.
 * TotAtm -> Number of atom in the IFF file.
 *
 * The returned value is the pointer of the bitmap that can be saved
 * directly in the IFF file.
 */

UBYTE *EncodeActiveAtm(UBYTE *Active, ULONG TotAtm)
{
    UBYTE           *PtrMtx;
    UBYTE           Bit;
    UBYTE           *Bitmap;
    ULONG           i;

    if ((Bitmap = (BYTE *)calloc(1, (TotAtm >> 3) + 1)) != NULL) {
        PtrMtx = Bitmap;
        Bit    = 1;
        for(i = 0; i < TotAtm; ++i) {
            if (Active[i]) *PtrMtx |= Bit;
            if (Bit == 128) {
                Bit = 1;
                ++PtrMtx;
            } else Bit <<= 1;
        } /* End of for */
    }

    return Bitmap;
}


/**** Decode the active atom from the bitmap ****/

/*
 * Active -> An array of unsigned bytes in which the boolean values
 *           are unpacked.
 * Bitmap -> The bitmap pointer.
 * TotAtm -> Number of atom in the IFF file.
 */

void PopActiveAtm(UBYTE *Active, UBYTE *Bitmap, ULONG TotAtm)
{
    ULONG          i;

    UBYTE          Bit = 1;

    for(i = 0; i < TotAtm; ++i) {
        Active[i] = ((*Bitmap & Bit) != 0);
        if (Bit == 128) {
            Bit = 1;
            ++Bitmap;
        } else Bit <<= 1;
    } /* End of for */
}

APPENDIX D - PDB Fat File Format 1.1

The PDB Fat (PDBF) file format is a custom version of the standard PDB that was created to include extra information, normally not allowed, keeping the compatibility with the Brookhaven National Library specifications. A sequence of REMARK records (one for each atom) was added at the beginning of file. The REMARK type is the user defined REMARK 77 (see PDB specifications) followed by the EXTRA keyword. This rule was introduced recognize the custom records from standard REMARKs. In each REMARK record are included the following information: atom number, element, atom type (according to force field) and the atomic partial charge:

         1         2         3         4
1234567890123456789012345678901234567890123
REMARK  77 EXTRA NNNNN EE FFFFFFFF  CC.CCCC

NNNNN    <- Atom number (C: %5d, Fortran: i5)
EE       <- Element (C: %-2.2s, Fortran: a2)
FFFFFFFF <- Atom type (C: %-8.8s, Fortran: a8)
CC.CCCC  <- Atom charge (C: %7.4f, Fortran: f7.4)

Warning:
Starting from 1.1 specifications, introduced in VEGA 1.5.0, the atom type format is changed in order to support atom types with more than four characters (the limit is now eight characters).  The old 1.0 specifications are supported by VEGA in read mode for backward compatibility.

Example:
Benzene ring with CVFF atom types and Gasteiger atom charges.

REMARK   4
REMARK   4 File converted by VEGA V1.1
REMARK   4
REMARK  77 EXTRA     1 C  cp    -0.0618
REMARK  77 EXTRA     2 C  cp    -0.0618
REMARK  77 EXTRA     3 C  cp    -0.0618
REMARK  77 EXTRA     4 C  cp    -0.0618
REMARK  77 EXTRA     5 C  cp    -0.0618
REMARK  77 EXTRA     6 C  cp    -0.0618
REMARK  77 EXTRA     7 H  h      0.0618
REMARK  77 EXTRA     8 H  h      0.0618
REMARK  77 EXTRA     9 H  h      0.0618
REMARK  77 EXTRA    10 H  h      0.0618
REMARK  77 EXTRA    11 H  h      0.0618
REMARK  77 EXTRA    12 H  h      0.0618
ATOM      1  C1  BEN     1       0.695   1.203   0.000  1.00  0.00
ATOM      2  C2  BEN     1      -0.695   1.203  -0.002  1.00  0.00
ATOM      3  C3  BEN     1      -1.389   0.000  -0.006  1.00  0.00
ATOM      4  C4  BEN     1      -0.695  -1.203  -0.007  1.00  0.00
ATOM      5  C5  BEN     1       0.695  -1.203  -0.006  1.00  0.00
ATOM      6  C6  BEN     1       1.389   0.000  -0.002  1.00  0.00
ATOM      7  H7  BEN     1       1.235   2.139   0.003  1.00  0.00
ATOM      8  H8  BEN     1      -1.235   2.139  -0.001  1.00  0.00
ATOM      9  H9  BEN     1      -2.470   0.000  -0.007  1.00  0.00
ATOM     10  H10 BEN     1      -1.235  -2.139  -0.010  1.00  0.00
ATOM     11  H11 BEN     1       1.235  -2.139  -0.007  1.00  0.00
ATOM     12  H12 BEN     1       2.470   0.000  -0.001  1.00  0.00
TER      13      BEN     1
CONECT    1    2    6    7
CONECT    2    1    3    8
CONECT    3    2    4    9
CONECT    4    3    5   10
CONECT    5    4    6   11
CONECT    6    1    5   12
CONECT    7    1
CONECT    8    2
CONECT    9    3
CONECT   10    4
CONECT   11    5
CONECT   12    6
MASTER       15    0    0    0    0    0    0    0   12    1   12    0
END

APPENDIX D - PDB ATDL 1.1

The PDB ATDL (PDBA) File Format is another special version of the standard PDB. This format was created in order to include extra information keeping the compatibility with the Brookhaven National Library specifications. For this reason, REMARK records (one for each atom) were added at the beginning of file to store the non-standard data. The REMARK type is the user defined REMARK 78 (see PDB specifications). This rule was introduced to recognize custom records from standatd REMARKs. In each custom REMARK, some information are included as: atom number, atomic charge, atom type (that is force field-dependent) and ATDL atom description. This last item isn't fully exhaustive, because it ends at second level of the ATDL description.

         1         2         3         4
1234567890123456789012345678901234567890
REMARK  78 NNNNN CCC.CCCC FFFFFFFF ATDL

NNNNN   <- Atom number (C: %5d, Fortran: i5)
CC.CCCC <- Atom charge (C: %8.4f, Fortran: f8.4)
FFFF    <- Atom type (C: %-4.4s, Fortran: a4)
ATDL    <- ATDL description (free format, see ATDL specifications)

Warning:
Starting from 1.1 specifications, introduced in VEGA 1.5.0, the atom type format is changed in order to support atom types with more than four characters (the limit is now eight characters).  The old 1.0 specifications are supported by VEGA in read mode for backward compatibility.

Example:
A3 molecule with TRIPOS atom types and Mopac atom charges.

REMARK   4
REMARK   4 File converted by VEGA V1.4.0
REMARK   4
REMARK  78     1  -0.1342 C.ar C-361 (C-361 C-361 H-100)
REMARK  78     2  -0.1211 C.ar C-361 (C-361 C-361 H-100)
REMARK  78     3   0.0103 C.ar C-361 (C-361 C-361 O-260)
REMARK  78     4   0.0127 C.ar C-361 (C-361 C-361 O-260)
REMARK  78     5  -0.1224 C.ar C-361 (C-361 C-361 H-100)
REMARK  78     6  -0.1317 C.ar C-361 (C-361 C-361 H-100)
REMARK  78     7   0.1346 H    H-100 (C-361)
REMARK  78     8   0.1490 H    H-100 (C-361)
REMARK  78     9   0.1495 H    H-100 (C-361)
REMARK  78    10   0.1351 H    H-100 (C-361)
REMARK  78    11  -0.2053 O.3  O-260 (C-361 C-460)
REMARK  78    12  -0.0061 C.3  C-460 (O-260 C-460 C-400 H-100)
REMARK  78    13  -0.0495 C.3  C-460 (C-460 O-260 H-100 H-100)
REMARK  78    14  -0.2028 O.3  O-260 (C-361 C-460)
REMARK  78    15   0.0983 H    H-100 (C-460)
REMARK  78    16   0.1358 H    H-100 (C-460)
REMARK  78    17  -0.0742 C.3  C-400 (C-460 N-300 H-100 H-100)
REMARK  78    18   0.1037 H    H-100 (C-460)
REMARK  78    19  -0.3024 N.3  N-300 (C-400 C-400 H-100)
REMARK  78    20   0.1057 H    H-100 (C-400)
REMARK  78    21   0.0759 H    H-100 (C-400)
REMARK  78    22  -0.0813 C.3  C-400 (N-300 C-400 H-100 H-100)
REMARK  78    23  -0.0242 C.3  C-400 (C-400 O-200 H-100 H-100)
REMARK  78    24   0.1049 H    H-100 (C-400)
REMARK  78    25   0.0725 H    H-100 (C-400)
REMARK  78    26  -0.1971 O.3  O-200 (C-400 C-361)
REMARK  78    27   0.0840 H    H-100 (C-400)
REMARK  78    28   0.0887 H    H-100 (C-400)
REMARK  78    29  -0.0066 C.ar C-361 (O-200 C-361 C-361)
REMARK  78    30   0.1008 C.ar C-361 (C-361 C-361 O-200)
REMARK  78    31  -0.2280 C.ar C-361 (C-361 C-361 H-100)
REMARK  78    32  -0.0676 C.ar C-361 (C-361 C-361 H-100)
REMARK  78    33  -0.2270 C.ar C-361 (C-361 C-361 H-100)
REMARK  78    34   0.0895 C.ar C-361 (C-361 C-361 O-200)
REMARK  78    35   0.1412 H    H-100 (C-361)
REMARK  78    36   0.1345 H    H-100 (C-361)
REMARK  78    37   0.1406 H    H-100 (C-361)
REMARK  78    38  -0.2037 O.3  O-200 (C-361 C-400)
REMARK  78    39  -0.0770 C.3  C-400 (O-200 H-100 H-100 H-100)
REMARK  78    40   0.1068 H    H-100 (C-400)
REMARK  78    41   0.0717 H    H-100 (C-400)
REMARK  78    42   0.0779 H    H-100 (C-400)
REMARK  78    43  -0.1905 O.3  O-200 (C-361 C-400)
REMARK  78    44  -0.0788 C.3  C-400 (O-200 H-100 H-100 H-100)
REMARK  78    45   0.1089 H    H-100 (C-400)
REMARK  78    46   0.0758 H    H-100 (C-400)
REMARK  78    47   0.0713 H    H-100 (C-400)
REMARK  78    48   0.1521 H    H-100 (N-300)
ATOM      1  C1  A3      1      -0.167   0.519  -0.316  1.00  0.00
ATOM      2  C2  A3      1       1.205   0.304  -0.310  1.00  0.00
ATOM      3  C3  A3      1       2.080   1.373  -0.177  1.00  0.00
ATOM      4  C4  A3      1       1.577   2.671  -0.061  1.00  0.00
ATOM      5  C5  A3      1       0.206   2.881  -0.062  1.00  0.00
ATOM      6  C6  A3      1      -0.667   1.809  -0.189  1.00  0.00
ATOM      7  H7  A3      1      -0.841  -0.318  -0.417  1.00  0.00
ATOM      8  H8  A3      1       1.601  -0.695  -0.405  1.00  0.00
ATOM      9  H9  A3      1      -0.173   3.887   0.035  1.00  0.00
ATOM     10  H10 A3      1      -1.733   1.980  -0.190  1.00  0.00
ATOM     11  O11 A3      1       3.444   1.107  -0.166  1.00  0.00
ATOM     12  C12 A3      1       4.203   2.182   0.346  1.00  0.00
ATOM     13  C13 A3      1       3.744   3.489  -0.311  1.00  0.00
ATOM     14  O14 A3      1       2.411   3.776   0.059  1.00  0.00
ATOM     15  H15 A3      1       3.813   3.412  -1.397  1.00  0.00
ATOM     16  H16 A3      1       4.382   4.319  -0.007  1.00  0.00
ATOM     17  C17 A3      1       5.678   1.886   0.076  1.00  0.00
ATOM     18  H18 A3      1       4.039   2.246   1.423  1.00  0.00
ATOM     19  N19 A3      1       6.547   2.933   0.612  1.00  0.00
ATOM     20  H20 A3      1       5.855   1.798  -0.997  1.00  0.00
ATOM     21  H21 A3      1       5.961   0.938   0.536  1.00  0.00
ATOM     22  C22 A3      1       7.967   2.742   0.320  1.00  0.00
ATOM     23  C23 A3      1       8.807   3.913   0.821  1.00  0.00
ATOM     24  H24 A3      1       8.092   2.633  -0.758  1.00  0.00
ATOM     25  H25 A3      1       8.294   1.815   0.791  1.00  0.00
ATOM     26  O26 A3      1      10.161   3.658   0.516  1.00  0.00
ATOM     27  H27 A3      1       8.681   4.035   1.898  1.00  0.00
ATOM     28  H28 A3      1       8.484   4.839   0.341  1.00  0.00
ATOM     29  C29 A3      1      10.955   4.719   0.921  1.00  0.00
ATOM     30  C30 A3      1      11.271   5.713   0.003  1.00  0.00
ATOM     31  C31 A3      1      12.069   6.782   0.410  1.00  0.00
ATOM     32  C32 A3      1      12.536   6.846   1.716  1.00  0.00
ATOM     33  C33 A3      1      12.215   5.847   2.625  1.00  0.00
ATOM     34  C34 A3      1      11.418   4.771   2.231  1.00  0.00
ATOM     35  H35 A3      1      12.341   7.576  -0.267  1.00  0.00
ATOM     36  H36 A3      1      13.151   7.677   2.027  1.00  0.00
ATOM     37  H37 A3      1      12.597   5.930   3.630  1.00  0.00
ATOM     38  O38 A3      1      11.039   3.720   3.067  1.00  0.00
ATOM     39  C39 A3      1      11.482   3.798   4.406  1.00  0.00
ATOM     40  H40 A3      1      11.115   2.931   4.956  1.00  0.00
ATOM     41  H41 A3      1      11.092   4.691   4.895  1.00  0.00
ATOM     42  H42 A3      1      12.572   3.787   4.458  1.00  0.00
ATOM     43  O43 A3      1      10.748   5.558  -1.281  1.00  0.00
ATOM     44  C44 A3      1      11.069   6.573  -2.210  1.00  0.00
ATOM     45  H45 A3      1      10.609   6.340  -3.170  1.00  0.00
ATOM     46  H46 A3      1      12.147   6.634  -2.365  1.00  0.00
ATOM     47  H47 A3      1      10.682   7.538  -1.882  1.00  0.00
ATOM     48  H48 A3      1       6.406   3.027   1.611  1.00  0.00
TER      49      A3      1
CONECT    1    2    6    7
CONECT    2    1    3    8
CONECT    3    2    4   11
CONECT    4    3    5   14
CONECT    5    4    6    9
CONECT    6    1    5   10
CONECT    7    1
CONECT    8    2
CONECT    9    5
CONECT   10    6
CONECT   11    3   12
CONECT   12   11   13   17   18
CONECT   13   12   14   15   16
CONECT   14    4   13
CONECT   15   13
CONECT   16   13
CONECT   17   12   19   20   21
CONECT   18   12
CONECT   19   17   22   48
CONECT   20   17
CONECT   21   17
CONECT   22   19   23   24   25
CONECT   23   22   26   27   28
CONECT   24   22
CONECT   25   22
CONECT   26   23   29
CONECT   27   23
CONECT   28   23
CONECT   29   26   30   34
CONECT   30   29   31   43
CONECT   31   30   32   35
CONECT   32   31   33   36
CONECT   33   32   34   37
CONECT   34   29   33   38
CONECT   35   31
CONECT   36   32
CONECT   37   33
CONECT   38   34   39
CONECT   39   38   40   41   42
CONECT   40   39
CONECT   41   39
CONECT   42   39
CONECT   43   30   44
CONECT   44   43   45   46   47
CONECT   45   44
CONECT   46   44
CONECT   47   44
CONECT   48   19
MASTER       51    0    0    0    0    0    0    0   48    1   48    0
END

APPENDIX D - Raw Surface Format

This file type is binary and endian-dependent. It's a sequence of fixed length records containing the information of each surface dot:

In C language, you can use the following structure to read/write the data:

struct vg_surface {
  unsigned int          Num;        /* Dot progressive number                 */
  unsigned int          AtmNum;     /* Atom number                            */
  float                 x, y, z;    /* Coordinates (don't change the order of */
  float                 Val;        /* these two fields)                      */
  char                  Color[3];   /* Color vector                           */
  char                  Flags;      /* Flags (not used yet)                   */
};

APPENDIX D –  VEGA SELECTION 2.0

The VEGA ZZ selection file (.sel) is used to store bonds, angles, distances, torsions, angles between two planes and multiple atom selections in a file to save the time required to do multiple analysis operations in which same selections are repeated several times (see the trajectory Selection Tool).

File format description:
Each record in the .sel file is defined by a case-insensitive keyword preceded by # character. The first line must be the file identification header:

#Selection 2.0

The #Selection keyword must be followed by file format version as argument and by selection records:

#<SELECTION_TYPE> <SELECTION_NAME>
<ATOM_1>
<ATOM_2>
...
<ATOM_N>

The <SELECTION_TYPE> is the selection type and can be: DISTANCE, ANGLE, TORSION, PLANEANGLE and MULTI. The <SELECTION_NAME> is the user-defined name of the selection. This must be an unique name for each selection type (e.g. two angles named Ang_1 can't exist, but one angle and one torsion with the same name are allowed). The <ATOM_1> to <ATOM_N> tags can be atom numbers or atom descriptors in standard VEGA format. For more information about atom selection rules, click here. The number of the <ATOM_N> lines is defined by the selection type, as shown in the following table:

Starting from 2.0 specifications, you can store in the TORSION record the parameters for the conformational search such as the starting torsion value (<BASE>), the number of steps (<STEPS>) in which the search is completed if it is a systematic conformational search, the rotation window (<END/WINDOW>) for the random searches or the end of the rotation for the systematic search and a Boolean flag (<ENABLED>) to take in consideration the torsion during the conformational search (for more details, see the AMMP dialog window):

#TORSION <SELECTION_NAME> <BASE> <STEPS> <END/WINDOW> <ENABLED>
 <ATOM_1>
 <ATOM_2>
 <ATOM_3>
 <ATOM_4>

All these parameters (coloured in red) are optional.

Example:
This is quisqua.sel file that can be used with quisqua.dcd trajectory placed in the Examples/Molecules directory.

#Selection 1.0

#DISTANCE "Dist_1"
N10:QUIS:1:*:1
O16:QUIS:1:*:1

#ANGLE "Ang_1"
C11:QUIS:1:*:1
C7:QUIS:1:*:1
C6:QUIS:1:*:1

#TORSION "Tor_1"
C7:QUIS:1:*:1
C6:QUIS:1:*:1
N3:QUIS:1:*:1
O2:QUIS:1:*:1

APPENDIX E - Language localization

Introduction:

In VEGA and VEGA ZZ, the language localization is provided by AmigaOS Locale Technology. This method allows to translate the character strings without recompile the source code, editing a text file and compiling it with a tool included in VEGA ZZ or in localization packages.
Each language requires a translation file (called catalog) which file name is that of the program that use it followed by  .catalog extension (e.g. VEGA.catalog, WINDD.catalog). The translation files must be placed in subdirectories named with the language (e.g. italiano, français, deutsch, etc) of the Catalogs folder that must be present in the program root directory .
All programs that uses this technology, can run without catalog files, because the default language (usually english) is built-in.

What you need to translate a catalog:

In order to translate all VEGA messages into your preferred language, you need the language localization (VEGA_XX_Locale.tar.gz) or the source code (VEGA_XX_Source.tar.gz) or VEGA ZZ package. If you are using the former package, please remember that the localization tools aren't installed if you performed the installation using the default settings. Before to start the translation, you must identify:

• FlexCat: the catalog builder.
  AmigaOS, Irix 6.2 Linux and  Windows 32 bit executables are included.  If your operating system is another one, you must compile the included source code (© Marcin Orlowski).

• Catalogs/VEGA.cd file.
  This is the text file used to generate the built-in language.

• Catalogs/VEGA.ct file.
  This is the catalog template to edit to do the translation.

• A text editor compatible with your operating system.

How to build a new VEGA.catalog file:

• Open the VEGA.ct file with your text editor.

• Change the first three lines:
  
  ## version $VER: XX.catalog XX.XX ($TODAY)
  ## language X
  ## codeset 0
  
  with:
  
  ## version $VER: VEGA.catalog 1.0 (compilation_date)
  ## language your_language
  ## codeset 0
  
  The compilation_date must be in DD.MM.YYYY format and your_language must be in lower case.

• In each blank line, translate the string in the next line. Please use ANSI/ISO character set only.

• Make sure to keep the C formatting characters in your translation (e.g. %s, %.4f, \n, etc).

• Save the VEGA.ct file.

• Build the VEGA.catalog typing:
  flexxcat VEGA.cd VEGA.ct CATALOG VEGA.catalog

• Copy VEGA.catalog to the suitable directory (e.g. Catalog/YOUR_LANGUAGE/). Please note that YOUR_LANGUAGE directory must be lower-case, otherwise the Unix systems can't find the file.

• Set LANGUAGE key of VEGA prefs file to YOUR_LANGUAGE. This step is needed for VEGA command line, if your operating system is Unix-like or if your PC doesn't recognize the operating system language. To change the language in VEGA ZZ, use the Preferences dialog.

Notes:

• For more information about FlexxCat, please consult the documentation included in the language package.

• The catalog file is a binary file with a standard IFF structure. More information about Interchange File Format (IFF) can be found in Native Developer Kit of Amiga Inc.

APPENDIX F - Dielectric constants

Typical dielectric constant values:

APPENDIX G - Error codes

This is the list of the error codes that can be reported by VEGA and VEGA ZZ

25. Copyright and disclaimers

All trademarks and software directly or indirectly referred in this document, are copyrighted from legal owners. VEGA and VEGA ZZ are freeware programs and can be spread through Internet, BBS, CD-ROM and other electronic formats. The Authors of these programs accept no responsibility for hardware/software damages resulting from the use of this package.
No warranty is made about the software or its performance.

These applications include SODIUM code developed by Alexander Balaeff at the Theoretical Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign.

Use and copying of these aplications  and the preparation of derivative works based on this software are permitted, so long as the following conditions are met:

• The copyright notice and this entire notice are included intact and prominently carried on all copies and supporting documentation.
    

• No fees or compensation are charged for use, copies, or access to this software. You may charge a nominal distribution fee for the physical act of transferring a copy, but you may not charge for the program itself.
    

• If you want include the VEGA packages into a commercial file collection, you must send a written request. The Authors can accept or deny the request on their own decision.
    

• If you change the source code to improve the VEGA performances, please contact the Authors to add your modifications in the official package.
    

• Any work distributed or published that in whole or in part contains or is a derivative of this software or any part thereof is subject to the terms of this agreement. The aggregation of another unrelated program with this software or its derivative on a volume of storage or distribution medium does not bring the other program under the scope of these terms.

Special VEGA ZZ notes:

VEGA ZZ requires the user registration to obtain the Activation Key generated starting from the Product Key. The Product and the Activation Keys are personal and work with a specific PC/workstation only. You can't activate more than one PCs with the same Activation Key because each PC has a different and unique Product Key. The activation expires after 1 year for non-profit academic users and after 30 days for business companies. After this time it's possible to request another Activation Key. The Authors can change the licensing method in any time on their own decision.
The business companies can't access to the collaborative support without purchasing the Support Pack: help or new feature requests will be trashed if they are from companies without Support Pack. The Authors spent a lot of time to develop a software that, in some cases, includes better performances than several commercial packages. They request a little contribution to the companies in order to continue the VEGA ZZ project otherwise destined to end in the near future.

VEGA and VEGA ZZ
are pieces of software developed in 1996-2021
by Alessandro Pedretti & Giulio Vistoli
All rights reserved.
 

Alessandro Pedretti
Dipartimento di Scienze Farmaceutiche
Facoltà di Scienze del Farmaco
Università degli Studi di Milano
Via Luigi Mangiagalli, 25
I-20133 Milano - Italy
Tel. +39 02 503 19332
Fax. +39 02 503 19359
E-Mail: info@vegazz.net
WWW: http://www.vegazz.net

1. Introduction

InpMerge is a shell command that can be used to merge the CHARMM/NAMD parameter files in order to obtain a single file. This is useful to when you need a parameter file containing custom data saved by the missing parameter table.

2. Installation & usage

The software is installed automatically with VEGA ZZ and it requires the locale.dll and the hdrive.dll to work properly. The program must  be executed from the command prompt, selecting VEGA ZZ -> VEGA Console in the Start menu.

Synopsis:

InpMerge   <OUTPUT>   <INPUT1>   <INPUT2> ...

3. History

• Release 1.0
  - First public release

4. Copyright and disclaimers

All trademarks and software directly or indirectly referred in this document, are copyrighted from legal owners. InpMerge is a freeware program and can be spread through Internet, BBS, CD-ROM and other electronic formats. The Authors of this program accept no responsibility for hardware/software damages resulting from the use of this package. No warranty is made about the software or its performance.

Use and copying of this software and the preparation of derivative works based on this software are permitted, so long as the following conditions are met:

• The copyright notice and this entire notice are included intact and prominently carried on all copies and supporting documentation.

• No fees or compensation are charged for use, copies, or access to this software. You may charge a nominal distribution fee for the physical act of transferring a copy, but you may not charge for the program itself.

• If you want include the InpMerge package into a commercial file collection, you must send a written request. The Authors can accept or deny the request on their own decision.

• If you change the source code to improve the InpMerge performances, please contact the authors to add your modifications in the official package.

• Any work distributed or published that in whole or in part contains or is a derivative of this software or any part thereof is subject to the terms of this agreement. The aggregation of another unrelated program with this software or its derivative on a volume of storage or distribution medium does not bring the other program under the scope of these terms.

InpMerge
is a software to merge the CHARMM parameter files
Copyright 2006-2023, Alessandro Pedretti & Giulio Vistoli
All rights reserved.

Alessandro Pedretti
Dipartimento di Scienze Farmaceutiche
Università degli Studi di Milano
Via Mangiagalli, 25
I-20133 Milano - Italy
Tel. +39 02 503 19332
Fax. +39 02 503 19359
E-Mail: info@vegazz.net
WWW: http://www.vegazz.net