13.3 Included scripts

 

13.3.1 Introduction

The VEGA ZZ package includes some scripts placed in ...\VEGA ZZ\Scripts directory with the following sub-directory structure:

Scripts
     _Templates (hidden folder)
  Ammp
  Build
  Calculation
Color
  Common
  Communication
  Database
  Docking
     AutoDock
    Vina
Examples
  File conversion
  Interaction surface
  Movie
Protein tools
Trajectory
Utilities

 

13.3.2 _Templates

This folder contains the templates used when a new script is created.

OpenGL.c 

Template for OpenGL C scripts.

    
Rebol.r  Template for REBOL scripts.
    
Stabdard.c Template for standard C scripts.
    
Window API.c Template window with Close button (Windows API version).
    
Window GraphApp.c Template window with Ok button (GraphApp GUI version).
    
Window GraphApp Calc.c Template window with Calculate button. Clicking this button, the main window hides and the abort dialog is shown. Pressing its Abort button, the calculation is stopped. This script template requires the GarphApp GUI.

 

13.3.3 Ammp

The scripts included in this directory, are useful to control some AMMP jobs in automatic way.

2D to 3D.c

Convert a structure from 2D to 3D, adding the hydrogens (if needed) and fixing the atom charges by Gasteiger - Marsili method if they aren't assigned. The procedure works in several steps:

  1. If needed, add the hydrogens with the more appropriate algorithm.

  2. Assign the atom charges.

  3. Send the molecule to AMMP.

  4. Gauss-Siedel distance geometry optimization (15 steps).

  5. Steepest descent energy minimization (50 steps, toler = 1).

  6. Conjugate gradients energy minimization (3000 steps, toler = 0.01).

  7. Send the resulting structure to VEGA ZZ.

Warning:
The script starts immediately asking nothing.

    
Dipole.c

Compute the dipole momentum by AMMP. If the charges aren't assigned, they are fixed by Gasteiger - Marsili method (see AMMP's DIPOLE command).

    
Interaction analysis.c Evaluate the non-bond interaction energy between two molecules. This calculation requires two molecules in the workspace: the first one must be the receptor and the second one must be the ligand. For more information, see ANALYZE command in AMMP manual.
The results are shown in VEGA ZZ console. AMMP shows the energy for each atom in the selection range:
Vnonbon internal lys.n 137 Eq -12.860423 E6 -1.397398 E12 2.191076
Vnonbon external lys.n 137 Eq 16.632879 E6 -5.806829 E12 9.177713
Vnonbon total lys.n 137 Eq 3.772456 E6 -7.204227 E12 11.368790

where internal is intramolecular energy, external is the intermolecular (interaction) energy, total is the sum of intramolecular and intermolecular energies, Eq is the electrostatic (coulombic) energy, E6 and E12 are the Lennard - Johnes terms. At the end of the atom dump, AMMP shows also:

Vnonbon total internal 151.439880
Vnonbon total external 2.272158
Vnonbon total 153.712067
153.712067 non-bonded energy
153.712067 total potential energy

where Vnonbon total internal is the total intramolecular energy, Vnonbon total external is the total intermolecular (interaction) energy, Vnonbon total is the total non-bond interaction energy (it's the sum of Vnonbon total internal and Vnonbon total external). Non-bonded energy and total potential energy are self explaining.

    
Neural network.c

Use the AMMP's Kohonen neural network to find the 3D space filling curve corresponding to the structure.  If the charges aren't assigned, they are fixed by Gasteiger - Marsili method (see AMMP's KOHONEN command).

    
Rigid docking.c

Perform the genetic algorithm rigid docking using AMMP. This calculation requires two molecules in the workspace: the first one must be the receptor and the second one must be the ligand. This last molecule is moved to obtain the complex. Both molecules must have the hydrogens and the charges are automatically fixed (Gasteiger - Marsili method) if they are unassigned.
This script has a graphic user interface (provided by GraphApp library) and to understand the meaning of each field, it's strongly recommended to read the GDOCK documentation.

 

13.3.4 Build

By these scripts, it's possible to build complex structures:

Aromaticity fix.c Fix the bond order in aromatic rings, changing the alternated single and double bonds to partial double bonds.
    
Coordinate transformation.c This script applies the specified transformation matrix to all atoms or to visible/active atoms only (see Active atoms only checlbox). It's useful to build multimeric structures from the information included in the REMARK 300 and 350 tags of PDB files.
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR
REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
REMARK 350
REMARK 350 GENERATING THE BIOMOLECULE
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 350   BIOMT1   2 -1.000000  0.000000  0.000000      174.00000
REMARK 350   BIOMT2   2  0.000000 -1.000000  0.000000      174.00000            
REMARK 350   BIOMT3   2  0.000000  0.000000  1.000000        0.00000

To build this homodimeric macromolecule:

  • Open the original PDB file.
  • Run Coordinate transformation script,
  • Put in the dialog window the values shown in red.
  • Click Apply button.
  • Reopen the original PDB file in the same workspace of the transformed structure and click Append in the dialog window.
    
Graphite.r Create one or more graphite planes.
    
Nanotube.r

Generates single-walled carbon nanotube (SWCNT) structures. It's based on VBS code developed by Roberto G. A. Veiga at Instituto de Física - Universidade Federal de Uberlândia (UFU) - Brazil, using the algorithm described in the article: White et al., Phys. Rev. B, 1993, Vol. 47, No. 9, pp. 5485-88.

    
Protonation fix.c Fix the protonation state of the molecule in the current workspace, removing the acid hydrogens (bonded to carboxylate, solphonate, phosphite and phosphate groups) and adding the basic hydrogens (to nitrogens of primary amines and guanidines).
    
Stereoisomers.c Build all possible stereoisomers from a chiral molecule that must be opened in the current workspace. Diastereoisomers are automatically minimized (conjugate gradients, 3000 steps, toler 0.01).
For security reasons, the maximum number of chiral centers is limited to 8 (28 = 256 stereoisomers), but it can be incresed to 32 changing the VGP_MAX_CHIRAL_CENTERS and VGP_MAX_CHIRAL_CENTERSSTR definitions.

When you start the script, a file requester is show in which you can put the output format and the file name that is used as prefix, because each stereoisomer is named adding the configuration of all stereocenters. You must remember that if the bond order of the starting molecule is assigned in wrong way, the chirality attribution could be incorrect (according to Cahn-Ingold and Prelog rules).
    
Zero coord.c

Place the atoms at the specified coordinates. Checking Active atoms only, only the visible atoms are moved.

 

13.3.5 Calculation

This directory includes scripts for generic calculations:

Copy properties.c Copy some molecular properties to the clipboard in selective mode.
    
Druglikeness.c Check the druglikeness of the molecule in the current workspace. Two methods are used:

 

Lipinski's rule of five
This rule establishes that  an orally active drug must have:

  • not more than 5 hydrogen bond donors (nitrogen or oxygen atoms with one or more hydrogen atoms);
  • not more than 10 (2 x 5) hydrogen bond acceptors (nitrogen or oxygen atoms) ;
  • a molecular weight under 500 g/mol ;
  • a partition coefficient logP less than 5.

Ghose's rule
This rule establishes that  an orally active drug must have:

  • partition coefficient logP in -0.4 to 5.6 range;
  • molar refractivity from 40 to 130;
  • molecular weight from 160 to 480;
  • number of heavy atoms from 20 to 70.

The molecular refractivity is calculated according to the Ghose and Crippen method.

 

References:
Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J.
"Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings"
AdV. Drug DeliVery ReV. 1997, 23,3-25.

Ghose, A. K.; Viswanadhan V. N.; Wendoloski, J.J.
"A Knowledge-Based Approach in Designing Combinatorial or Medicinal Chemistry Libraries for Drug Discovery. 1. A Qualitative and Quantitative Characterization of Known Drug Databases"
J. Comb. Chem. 1999, 1, 55 68.

    
Elecrostatic energy.c

Evaluate the electrostatic energy of the molecule in the current workspace. The default dielectric constant is 1 (vacuum).

    
Mopac.r  Run multiple Mopac jobs.

 

13.3.6 Color

Scripts to color the molecule:

Color RasMol.c Color the molecule using the RasMol color scheme.
   
Color VMD.c

Color the molecule using the VMD color scheme.

 

13.3.7 Common

This directory contains the initialization scripts to include in REBOL scripts:

Fmod.r Fmod commands.
    
Formats.r File format keywords and other definitions.
    
Utils.r Functions for path manipulation.
    
Vega.r VEGA ZZ interface (don't change it without any real reason !).
    
Vutils.r REBOL/View utilities.

The C header files contained in this directory are hidden and they can't changed directly by VEGA ZZ environment.

 

13.3.8 Communication

This directory includes communication and Internet-related scripts:

ActiveSync VRML send.c

Convert the molecule in the current workspace to VRML and send it to mobile devices (e.g. PocketPC) using Microsoft ActiveSync. The molecule can be shown using a pocket VRML viewer (e.g. Pocket Cortona). Due to the mobile device hardware limits, don't transfer too complex molecules. The script requires Microsoft ActiveSync and it works with all Windows versions.

    
E-mail PDB send.c Save the molecule in PDB format, compress it and attach it to a user-editable e-mail. This script uses the MAPI layer and so it's compatible with MAPI compliant e-mail clients only (e.g. Outlook, Outlook Express, etc). To change the output format or other settings, see the script source code.
    
FTP put.r

Copy the molecule in the current workspace to a remote host via FTP.

    
IrDA VRML send.c

Convert the molecule in the current workspace to VRML and send it to mobile devices (e.g. PocketPC) over an infrared link. The molecule can be shown using a pocket VRML viewer (e.g. Pocket Cortona). Due to the mobile device hardware limits, don't transfer too complex molecules. The script requires at least Windows 2000.

    
Web server.r

Micro Web server for on-line manual.

 

13.3.9 Database

This directory includes scripts to manage databases:

Database expander.r It's a REBOL/View script to extract the molecules contained in a database to a directory. It allows to specify the file format, the compression and the save attributes (connectivity and constraints). 
    
Database logP.c Calculate the logP by Testa's MLP method for each molecule in the database and export the results in a CSV (Output file) file. The input must be a supported database (Input database) and its structures can be pre-processed adding the hydrogens (Add the hydrogens) applying the geometry method (default) or the bond order method (Use bond order). This last method is recommended if the molecules have an assigned bond order. In the pre-processing phase, the structures can be optimized by the steepest descend (Steepest minimization) and/or the conjugate gradients (Conjugate minimization) methods. For both minimization algorithm, it's possible to put the number of iterations (Steps), the toler value (Toler) and the dielectric constant (Dielectric). Checking Update the graphic, the 3D graphic output is updated every 20 minimization steps. Increasing the Dot density value, it's possible to make a better prediction of the logP. A good value is from 10 to 50 dots for Å2.

 

Warning:

even if in the theory it's possible to manage a 2D database, adding the hydrogens by the bond order method and optimizing the structures, this procedure is not recommended because the distance geometry optimization is not performed. For this reason, a better choice is the conversion of the database from 2D to 3D (see the Database 2D to 3D.c script) and the resulting database can be used directly to predict the logP values.

    
Database volume.c Calculate the volume of each molecule in the database. It have the same options of the Database logP.c script.
    
Database to 0D.c Convert a 2D or 3D database to a 0D SDF database, translating all atoms at the specified coordinates, usually at (0, 0, 0).
    
DrugBank SDF fix.c The DrugBank SDF files aren't standard, because the header of each reacord has two lines only instead of three and the first line contains a tab character to delimit the molecule name from the DrugBank ID.
This script create a new file adding _fix.sdf suffix to the file name and fixing the files adding the missing line, removig the tab character and "SDF file of " string in the molecule name line.
    
SDF metadata extractor.c This script extracts the metadata (e.g. InChi, SMILES, biological activity, etc) from a SDF file and puts it into a Comma Separated Values (CSV) file. The output file is placed in the same directory of the source database and its name is generated from it adding _meta.csv suffix.
    
SMILES to database.c This script converts the SMILES molecules of a CSV file to 3D and puts them in a database. The CSV file must have two fields for each line separated by a semicolon (;): the former must be the molecule name and the latter must be the SMILES string.
    
Subset creator.c Create a new database in SQLite format, including a subset of molecules of another database. The molecules must be specified in a text file in which molecule names (not ID) are placed one for each line.
The subset database is created in the same directory of the source preserving its name as prefix and adding _subset.db suffix. A log file is generated also in which  possible problems are reported.

This script was specially developed to prepare input databases for virtual screening studies.

 

13.3.10 Docking

Scripts for molecular docking.

 

13.3.10.1 AutoDock

These scripts allow to prepare input files for AutoDock 4:

Box calc.c Calculate the box dimensions and its center coordinates containing the active (visible) atoms and show the results in the console. This script is useful to define a macromolecule region to dock ligands.
    
DLG to PDB multimodel.c Convert an AutoDock 4 DLG output to a standard PDB multimodel file, keeping in the remarks the energy information. This conversion is not required by VEGA ZZ that read DLG files as trajectories, but is needed by programs that are unable to manage this kind of files.
    
Ki calculator.c Evaluate the Ki and the interaction energy of a given ligand - receptor complex. This script is useful to recalculate the AutoDock 4 score after an energy minimization (e.g. performed by NAMD). This calculation requires two molecules in the workspace (the first one must be the receptor and the second one must be the ligand) and atom constraints defining the region in which the AutoDock 4 grid map is calculated. The free atoms only are considered to define this region.

Warning:
You could find problems with UNC network path (e.g. \\myserver\my directory) because it's not fully supported by cygwin.dll library. For this reason, run AutoGrid saving the files on your local disk.
    
Ligand.c Prepare and save the current molecule as receptor for AutoDock 4, performing these steps:
  1. If needed, add the hydrogens by protein method.
  2. If required, assign the atom charges.

If the molecule has two dimensions only, the 2D to 3D conversion is performed as explained below:

  1. Send the molecule to AMMP.
  2. Gauss-Siedel distance geometry optimization (15 steps).
  3. Steepest descent energy minimization (50 steps, toler = 1).
  4. Conjugate gradients energy minimization (3000 steps, toler = 0.01).
  5. Send the resulting structure to VEGA ZZ.

These steps are performed for both 2D and 3D structures:

  1. Fix the atom types, applying the AutoDock force field.
  2. Remove the apolar hydrogens.
  3. Save the molecule in PDBQT format.
    
Receptor.r Prepare and save the molecule in the current workspace as receptor for AutoDock 4, performing these steps:
  1. If needed, add the hydrogens by protein method.
  2. If required, assign the atom charges.
  3. Fix the atom types, applying the AutoDock force field.
  4. Remove the apolar hydrogens.
  5. Save the molecule in PDBQT format.
  6. Run AutoGrid4 to calculate the maps if the user confirms the operation.

The pre-defined docking box is set to explore the entire receptor, but if you want explore a specific protein region, you must select the atoms defining that region before to run the script.
The grid spacing is automatically adjusted if the number of grid points exceeds the 63 value because AutoGrid 4 and AutoDock 4 can't manage grid greater than 63x63x63 points.

 

13.3.10.2 Vina

These scripts allow to prepare input files and to run AutoDock Vina:

Docking.c This script performs a molecular docking calculation using AutoDock Vina. The receptor and the ligand files must be in PDBQT format and can be prepared by Receptor.c and Ligand.c scripts. In the graphic interface of this script, you can specify the following parameters:
  • Receptor
    File name of the target macromolecule (receptor) in PDBQT format.
  • Ligand
    File name of the ligand to dock in PDBQT format.
  • Output model
    File name of the ligand poses in PDBQT multimodel format. Remember that this file doesn't include the receptor structure.
  • Log file
    Vina log file name.
  • Center
    X, Y, Z coordinates of the binding site center.
  • Size (Å)
    Dimensions in Å of the cube including the binding site.
  • Exahaustiveness
    Exhaustiveness of the global search (roughly proportional to time).
  • Binding modes
    Maximum number of binding modes to generate.

For more information about AutoDock Vina, click here.

    
Ligand.c Prepare and save the current molecule as receptor for Vina, performing these steps:
  1. If needed, add the hydrogens by protein method.
  2. If required, assign the atom charges.

If the molecule has two dimensions only, the 2D to 3D conversion is performed as explained below:

  1. Send the molecule to AMMP.
  2. Gauss-Siedel distance geometry optimization (15 steps).
  3. Steepest descent energy minimization (50 steps, toler = 1).
  4. Conjugate gradients energy minimization (3000 steps, toler = 0.01).
  5. Send the resulting structure to VEGA ZZ.

These steps are performed for both 2D and 3D structures:

  1. Fix the atom types, applying the Vina force field.
  2. Remove the apolar hydrogens.
  3. Save the molecule in PDBQT format.
    
Receptor.c Prepare and save the molecule in the current workspace as receptor for Vina, performing these steps:
  1. If needed, add the hydrogens by protein method.
  2. If required, assign the atom charges.
  3. Fix the atom types, applying the Vina force field.
  4. Remove the apolar hydrogens.
  5. Save the molecule in PDBQT format.
    
Virtual screening.c This script performs structure-based virtual screenings by AutoDock Vina. To do them, you need:
  • the receptor structure in PDBQT format. You can prepare it from any type of file using Receptor.c script;
  • the database containing the ligands to screen. It must be in any format supported by VEGA ZZ (Microsoft Access, ODBC data source, SDF file, SQLite and Zip archive). The database don't require to be prepared before the screening, because the script has the capability to detect the missing features and to fix them. In particular, it can add hydrogens using the best strategy, fix the atomic charges and to convert structures from 2D to 3D.

The graphic user interface of this script allows to setup the screening in easy way, changing the following parameters:

  • Receptor
    File name of the target macromolecule (receptor) in PDBQT format.
  • Energies
    Output file in localized CSV format containing the energy of the best pose for each ligand. The first column is the molecule progressive number (MolID), the second one is the molecule name (Name) and the third one is the Vina energy of the best pose (Energy).
  • Ligand database
    Database of the ligands to screen.
  • Output models
    File name of the Zip archive in which the poses in PDBQT multimodel format are stored. The script add a numerical suffix to file name that is incremented automatically every time in which the file size exceeds the limit of 2 Gb.
  • Log file
    Log file name.
  • Center
    X, Y, Z coordinates of the binding site center.
  • Size (Å)
    Dimensions in Å of the cube including the binding site.
  • Exhaustiveness
    Exhaustiveness of the global search (roughly proportional to time, default 8).
  • Binding modes
    Maximum number of binding modes to generate (default 1).

    Clicking Calc button, Center and Size fields are automatically completed using the atoms selected in the current workspace that will be considered as binding site.
    Clicking Save cfg, you can save the current configuration that can be restored clicking Load cfg. The resulting .vcf file is not compatible with Vina, while that generated by Docking.c maintains the compatibility (see --config option of Vina).

    For more information about AutoDock Vina, click here.

If you want to run a Vina docking calculation, follow these steps:

 

13.3.11 Examples

This directory includes the example scripts:

Benzene.bat Build a benzene ring using the extended commands.
    
Benzene.c Same of above but written in C.
    
Benzene.htm Same of above but written in JavaScript.
    
Benzene.r Same of above but written in REBOL.
    
Command console.htm This script demonstrates how it's possible to control VEGA ZZ by JavaScripts in a HTML page.
    
Demo.bat Demo script.
    
Demo.r The same of the above, but written in REBOL.
    
Distances.r This REBOL script explains how to measure interatomic distances.
    
Graph.r Demo of the extended commands to manage the plots.
    
GraphApp demo.r Demo of the GraphApp GUI library.
    
Info.r  Show some information in the VEGA ZZ console.
    
Meshload.r Load & display a 3D rabbit mesh model.
    
MP3 player.r Minimalist mp3 player (fmod demo).
    
Requesters.r Simple demo of the VEGA ZZ built-in requesters.
    
VEGA GL.c Application example of VEGA GL commands.
    
View\VEGA ZZ toolbar.r Show a REBOL/View toolbar to control the VEGA ZZ main features.

 

13.3.12 File conversion

This directory includes scripts for file format conversion :

CSSR SOMFA export.c Export the current molecule in CSSR format readable by SOMFA.
    
CSV export.c Save the molecule in Comma Separated Values (CSV) format.
    
Format conversion.r 

This script performs the batch file format conversion of all molecules contained in a folder. Some parameters can be changed in the dialog window:

  • Source dir.
    Name of the source directory in which the converting files are placed. Click Open button to show the directory requester.
  • Destination dir.
    Name of the destination directory in which all converted files will be inserted. Click Open button to show the directory requester.
  • Output format
    Use this list to select the output format.
  • Compression
    Compression method (default none).
  • Add hydrogens
    - None
    No hydrogens will be added.
    - Generic
    Generic organic geometry-based method.
    - Generic BO
    Generic organic bond order-based method.
    - Nucleic acid
    Nucleic acid geometry-based method.
    - Nuc. acid BO
    Nucleic acid bond order-based method.
    - Protein
    Protein geometry-based method.
    - Protein BO
    Protein bond order-based method.
  • Include the connectivity
    If checked, the atom connectivity is included (if the file format supports it).
  • Include the atom constraints
    If checked, the atom constraints are saved into the file (if the file format supports it).
  • Normalize the coordinates
    If checked, the molecule is translated at the axis origin (0, 0, 0).
  • Assign the Gasteiger/Marsili charges
    If checked, the Gasteiger - Marsili atom charges are assigned.

    Clicking Convert button, the conversion starts and clicking Close the dialog window is closed.
    
PDB ren export.c Export the molecule in PDB format renumbering the atoms.
    
XYZ import.c Import XYZ files giving the possibility to adapt the filter to each sub-format.

 

13.3.13 Interaction surface

These scripts calculate and manage ligand-receptor interaction surfaces.

CHARMM interaction surface.c Calculate the CHARMM non-bond interaction energy of each ligand-receptor atom pair and project it on the Van der Waals surface. The user must enter the molecule ID/number to indicate the ligand.
    
Lipophilic interaction surface.c Calculate the lipophilic interaction of each ligand-receptor atom pair and project it on the Van der Waals surface. The user must enter the molecule ID/number to indicate the ligand.
    
MEP interaction surface.c Calculate the electrostatic interaction energy of each ligand-receptor atom pair and project it on the Van der Waals surface. The user must enter the molecule ID/number to indicate the ligand.
    
MLPInS color ramp.c This script normalizes the color ramp calculated by MLPInS interaction surface script, using the user-defined range of values. The normalization is useful to compare surfaces of different molecules using the same color scheme.
It recognizes MLPInS surfaces only and changes them selectively.
   
MLPInS interaction surface.c Calculate the MLP Interaction Score (MLPInS) of each ligand-receptor atom pair and project it on the Van der Waals surface. The user must enter the molecule ID/number to indicate the ligand.

 

13.3.14 Movie

Scripts to create movies.

Movie maker.c This script generates a movie file starting from the molecule in the current workspace, rotating it around one or more axis. The parameters that the user can change are: Output movie (file name of the output movie), Number of frames (number of frames to put in the trajectory),Preview (checking this gadget, the animation is shown in the main window not saving the output movie), X rotation (rotation in degrees around the X axis), Y rotation (rotation in degrees around the Y axis) and Z rotation (rotation in degrees around the Z axis).
Clicking Animate, the movie will be created. The codec requester is shown to select the required compression options. Take care choosing the Render mode because not all graphic cards supports the Hardware mode. The Software rendering is the most reliable even if it's unable to reach the Hardware quality.
    
Sec. structure anim.c This script generates a movie file starting from the peptide in the current workspace, changing the secondary structure. The parameters that you can change are: Output movie (File name of the output movie), Number of frames (number of frames to put in the animation), Preview (checking this gadget, the animation is shown in the main window not saving the output movie), Start Phi (starting value of the Phi dihedral angle), Start Psi (starting value of the Psi dihedral angle, Start Omega (starting value the Omega dihedral angle), End Phi (ending value of the Phi dihedral angle), End Psi (ending value of the Psi dihedral angle), End Omega (ending value of the Omega dihedral angle).
Click Animate to create the movie file. The codec requester is shown to select the required compression options. Take care choosing the Render mode because not all graphic cards supports the Hardware mode. The Software rendering is the most reliable even if it's unable to reach the Hardware quality.
For the most common Phi, Psi and Omega values, click here.

 

13.3.15 Protein tools

This directory includes the visualization scripts:

Aminoacid selector.r

Show the aminoacid by selection and/or by chemical/physical properties.

    
Dump backbone torsions.c Dump the phi and psi backbone torsions of a protein.
    
Fasta to text.r

Convert a Fasta into a text file. That's is useful to load it into Microsoft Excel.

    
Fred2 scrore.c Calculate the interaction score of a ligand - protein complex using OpenEye's Fred2 docking software. This calculation requires two molecules in the workspace: the first one must be the receptor and the second one must be the ligand. The scores extracted from Fred's outputs are: Chemgauss2, Chemscore, Plp, Screenscore, Shapegauus and Zapbind. The results are automatically copied to the clipboard.

 

Warning:

This script requires Fred2 installed on your PC. You can request/buy it at http://www.eyesopen.com/

    
HIS protonantion.c

Find the histidine protonantion state (on NE2 or on ND1) using the CHARMM potential and swap the hydrogens (e.g. H-NE2 to H-ND1) according to the hydrogen bond energy. If the energy difference between the H-NE2 and H-ND1 tautomers is more than 2.0 Kcal/mol the hydrogen is placed on the nitrogen realizing a structure with lower hydrogen bonding energy. The starting structure must have the hydrogens.

    
Move hydrogens to end.c

Move the hydrogens to the end of the atom list. In this way, you can obtain files split in two parts: the first one containing the heavy atoms and the second one, placed at the end, containing the hydrogens. As an example, that's useful to write mol2 files compatible with GOLD docking system.

    
Remove apolar hydrogens.r

Remove the apolar hydrogens from the current structure.

    
Score.c Calculate the interaction score between a ligand and a generic target biomacromolecule. The ligand must be previously docked in the target structure. This calculation requires two molecules in the workspace: the first one must be the receptor and the second one must be the ligand.
The script can calculate:
  • Electrostatic energy (Coulomb).
  • Electrostatic energy with distant-dependent dielectric constant.
  • R6-R12 Lennard-Johnes non-bond energy using the CHARMM and CVFF force fields.
  • Hydrophobic interaction using the Broto-Moreau parameters with different distance functions (linear, square, cube and Ferm's function).

The results are automatically copied to the clipboard.

 

13.3.16 Trajectory

It contains scripts for trajectory management.

Anim maker.c This script generates a trajectory file starting from the molecule in the current workspace, rotating it around one or more axis. That's useful to create video files. The parameters that the user can change are:
  • Output trajectory
    File name of the output trajectory. In the file requester, is it possible to select the output format (default Gromacs XTC).
  • XTC comp. (1-6)
    Gromacs XTC compression ratio. It has a meaning only if the Gromacs XTC format is selected as output (default 3).
  • Save the animation
    Check this gadget to save/render the animation (e.g. avi, mpeg, etc).
  • Number of frames
    Number of frames to put in the trajectory (default 50).
  • X rotation
    Rotation in degrees around the X axis (default 0). Negative values are allowed.
  • Y rotation
    Rotation in degrees around the Y axis (default 360). Negative values are allowed.
  • Z rotation
    Rotation in degrees around the Z axis (default 0). Negative values are allowed.
  • Animate
    Push this button to create the animation trajectory.
     
    
Automatic quenching.r This script extracts the frames from a trajectory file, then minimize them using AMMP or Mopac. The results will be stored to an output trajectory file. You can input some parameters:
  • Input molecule
    File name of the input molecule. When you select a molecule using Open button, Input trajectory, Output trajectory and Output energy fields are automatically updated.
  • Input trajectory
    File name of the input MD trajectory. When you select a new trajectory using Open button, Output trajectory and Output energy fields are automatically updated.
  • Output trajectory
    File name of the output trajectory. When you select a new trajectory using Open button, Output energy field is automatically updated. In the file requester, you can select the output format.
  • XTC comp. (1-6)
    Gromacs XTC compression ratio. It has a meaning only if Gromacs XTC format is selected as output.
  • Output energy file
    File in which the energy values are stored (CSV format). It's available only if Mopac is selected as Minimization type.
  • First frame
    Trajectory frame from which the quenching starts.
  • Last
    Trajectory frame to which the quenching ends.
  • Step
    Increment for the frame enumeration.
  • Minimization type
    This field allows to select the minimization type: None (nothing is performed), AMMP (molecular mechanics method based on the conjugate gradients algorithms) and Mopac (semiempirical method).
  • AMMP min. steps
    Number of minimization steps used by AMMP.
  • AMMP toler
    I's the convergence criterion used by AMMP to stop the minimization.
  • Mopac keywords
    In this field, you can put the keywords to control the Mopac calculation.
  • Calculate
    Press this button to perform the quenching. If a parameter is incorrect or missing, an error message is shown.
    
DCD fix for VMD.c All pre-3.0.0 VEGA ZZ releases write buggy DCD files that aren't readable by VMD. This scripts fix the problem patching the DCD trajectory only if the problem is detected.
    
Dump energy.c This script calculates the energy for each MD frame and dumps the molecular mechanics energy components in a CSV file. It also performs a histogram analysis.
  • Input molecule
    File name of the input molecule. When you select a molecule using Open button, Input trajectory, Output trajectory and Output energy fields are automatically updated.
  • Input trajectory
    File name of the input MD trajectory. When you select a new trajectory using Open button, Output trajectory and Output energy fields are automatically updated.
  • Output energy
    Output energy file in CSV format (Comma Separated Values). Each column contains the following data: frame number, bond, angle, torsion, hybrid, non-bond and total energies.
  • Output histogram
    Output histogram in CSV format.
  • First frame
    Trajectory frame from which the quenching starts.
  • Last
    Trajectory frame to which the quenching ends.
  • Step
    Increment for the frame enumeration.
  • Minimization type
    This field allows to select the minimization type: None (nothing is performed), AMMP (molecular mechanics method based on the conjugate gradients algorithms) and Mopac (semiempirical method).
  • AMMP min. steps
    Number of minimization steps used by AMMP.
  • AMMP toler
    I's the convergence criterion used by AMMP to stop the minimization.
  • Mopac keywords
    In this field, you can put the keywords to control the Mopac calculation.
  • Calculate
    Press this button to perform the quenching. If a parameter is incorrect or missing, an error message is shown.
    
Enantiomerizer.r Convert the trajectory to another format inverting all chiral atoms. You can specify the following parameters:
  • Input traj.
    File name of the input trajectory. Clicking Open button, the file requester is shown.
  • Output traj.
    File name of the output trajectory.
  • Output format
    File format of the output trajectory.
  • Compression
    Compression level. It has an effect only if XTC format is selected.
  • Append if the file exists
    If it's checked and the output trajectory exists, the converted frames are appended.
  • Consider selected atoms only
    If it's checked, the active (visible) atoms only are saved into the new trajectory.
  • Swap endian
    If it's checked, the endian of the converted trajectory is swapped. This function has an effect only if the DCD format is selected.

Click Go ! button to start the conversion and Cancel button to close the window.

    
Frame extractor.r Extract the frames from a trajectory file (Input Traj.), saving them in the specified directory (Output Dir.). You can change Quenching step, Output format and Compression method.
    
Ramachandran.c

This script perform the Ramachandran analysis for each trajectory frame. Before running it, you must open a trajectory file. For each frame, the Phi and Psi backbone torsion angles are measured and evaluated if they are inside or outside the Ramachandran permission areas. For each frame is calculated the percentage referred to the total number of the residues and these values are visualized in a plot. This calculation is useful to highlight the secondary structure evolution during a MD simulation. If the percentage of the residues (Phi and Psi values) inside the permission areas is decreasing during the simulation, it means that the secondary structure evolves to a worse situation. Vice versa, if the percentage is growing, the secondary structure is improving.

    
SDF export.c Convert the current trajectory in a SDF database. Each structure in the database is equivalent to each frame in the trajectory file.
    
Water remover.r

Remove all water molecules from a trajectory converting it into a PDB multimodel file. This script is obsolete and it's maintained as example only. The same function is now implemented in VEGA ZZ without external scripts. 

 

13.3.17 Utilities

This directory includes the generic scripts. Some of these require REBOL/View.

Calculator.r Simple calculator (script by Ryan S. Cole).
    
Calendar.r Calendar and scheduler (script by Sterling Newton).
    
Clock.r Digital clock (script by Carl Sassenrath).
    
Console.r Open the REBOL console.
    
Image viewer.r Image viewer.