VEGA ZZ is the evolution of the well known VEGA OpenGL package and includes several new features and enhancements making your research jobs very easy. VEGA was originally developed to create a bridge between most of the molecular software packages only, but in the years, enhancing its features, it's evolved to a complete molecular modelling suite. This software is FREE for non-profit academic uses.

Extreme OpenGL implementation for an incredible real-time rendering quality: lighting (4 customizable light sources + ambient light), alpha blending, hardware anti-aliasing, material management, 3D backgrounds.

Stereo view (shutter or anaglyphic  glasses).

Hardware and software offline rendering.

3D molecule view: wireframe with multivector bonds, CPK, ball & stick, stick, trace and tube. All representations can be mixed thanks to the selection tool.

Atom labels.

Enhanced atom coloring methods.

Atom selection & picking.

3D surface: dotted, mesh, solid, solid transparent. Thanks to the HyperDrive technology, the calculation is very fast. The surfaces can be colored by atom, residue, chain, segment, molecule, surface ID and property. The color gradient used in the property coloring mode can be customized by the user defining the number and the type of colors.

Multiple surface management.

All 3D object can be managed with mouse, joystick and dials.

3D interactive monitors calculated in real time (distance, angle, torsion and angle between two planes).

Simulation trajectory visualization and animation.

Snapshot, hardware and software image rendering with the capability to create images bigger than the monitor size. The software rendering includes an anti-aliasing algorithm with user-selectable 4x or 16x super sampling. The supported output formats are: BMP, GIF 256 colors, JPEG, PCX, PNG, PNM, RAW, SGI, TGA and TIFF.

Vector graphic rendering engine. It's possible to export the view in LaTex, PostScript, Encapsulated PostScript, PDF, POV-Ray, SVG and VRML 2.0 formats.

Native video compression for animations: the trajectory files can be converted in real animation files (AVI, MPEG-1 and MPEG-2) without external software. VEGA uses the Windows codecs for the standard AVI files and a built-in library to encode MPEG-1 & 2 streams. The MD animations can be converted in DVD, Super Video CD, Video CD and video streams for the Web in easy way.

Slow motion feature converting the trajectory files to video streams.

File merge: VEGA ZZ is able to merge files in different formats, in order to take selectively coordinates, parameters, fields and properties of each file.

Trajectory file manipulation: the MD flies can be converted in other formats removing/skipping frames. The supported output formats are: NAMD/CHARMM DCD, Gromacs XTC (the compression ratio is user-selectable), IFF/RIFF (32 and 64 bit), Mol2 multi-model and PDB multi-model.

Molecular mechanics provided by AMMP: energy minimization (single point, steepest descent, trust, conjugate gradients, quasi-Newton, truncated Newton, genetic algorithm, polytope simplex and rigid body), 0D to 3D and 2D to 3D conversion, interaction analysis, neural network to find the 3D space filling the curve corresponding to the structure, rigid docking.

Conformational search: grid scan, random search and Boltzmann jump. VEGA ZZ is able to find automatically the flexible torsions.

Molecular dynamics provided by NAMD (not included in the package, but available for free at http://www.ks.uiuc.edu/Research/namd/). The most common function are accessible trough the graphic interface and the simulation can be interactively launched in the VEGA ZZ environment.

Analysis of molecular dynamics trajectory files (distances, angles, torsions, angles between two planes, dipole moment, ILM, MLP, lipole, PSA, RMSD, surface area, surface diameter, volume and volume diameter).

Cluster analysis of the molecular dynamics and conformational search trajectory files (cluster by coordinates, by torsion and by torsion RMSD).

Graphic interface for Mopac 7, included in the package, and Mopac 2007, not included but available at:
http://openmopac.net/MOPAC2007.html

Interactive protein check (chirality, peptidic bond geometry, missing residues and ring intersection).

Molecule (input): Alchemy, Accelrys Insight .car and .arc, Accelrys Quanta/CHARMm CRD, CSR, MSF and DCD, AMMP, BioDock output, Cambridge Data File (CSSR), Cartesian coordinates (XYZ), Chem3D, ChemSol, CML 1.0 and 2.0, CPMD XYZ, ESCHER NG solutions, Fasta, GAMESS cartesian input and output, Gaussian cartesian input and output, Gromos/Gromacs .gro and .xtc, Gaussian input and output, HyperChem .hin, Interchange File Format (IFF/RIFF 32 and 64 bit), IIUCr Crystallographic Information Framework (CIF, mmCIF), UMSC CRT, QMC, MDL Molfile, MDL Extended Molfile (V3000), Mopac internal coordinates, Protein Data Bank (PDB), Data Bank with ATDL atom types (PDBA), Protein Data Bank Fat (PDBF), Protein Data Bank MultiModel, Tinker XYZ, Tripos Sybyl (Mol2), X-Plor PSF.

Molecule (output): Accelrys Insight .car (archive 1 and 3), Accelrys Quanta/CHARMm CRD and MSF, Alchemy, AMMP, Cambridge Data File (CSSR), Cartesian coordinates (XYZ), ChemSol, CML 1.0 & 2.0, CPMD XYZ, Fasta, GAMESS cartesian, Gaussian cartesian input, Gromos/Gromacs .gro, Interchange File Format (IFF), IUCr Crystallographic Information Framework (CIF, mmCIF), IUMSC CRT, MDL Molfile,  MDL Extended Molfile (V3000), Mopac cartesian coordinates, Mopac internal coordinates, 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 Large (> 99999 atoms, PDBL), Protein Data Bank simplified, PQR, Tripos Sybyl (Mol2), X-Plor PSF.

Trajectory: Accelrys archive file (.arc), AutoDock 4 DLG output, BioDock output, Crystallographic Information Framework multi-model (CIF, mmCIF), CSR (Accelrys conformational search), DCD (CHARMM, NAMD), ESCHER NG, Gromacs TRR, Gromacs XTC, IFF/RIFF (32 and 64 bit), MDL Mol multi-model, Mol2 multi-model and PDB multi-model file formats.

The REBOL scripting language is included in the package for batch processing, multiple calculations and  multiple host communication.

C script engine: you can create super-fast scripts in C language directly in the VEGA ZZ environment. They are built in real time by Tiny C compiler included in the package.

Support for standard batch files trough SendVegaCmd command.

Automatic topology and parameter check in order to find the missing parameters before the MM/MD run. This features is very useful for NAMD calculations with non standard topologies.

HyperDrive technology  to take full advantages of multiprocessor systems, Hyper Threading CPUs (e.g. Pentium 4) and multi-core CPUs (e.g. Athlon X2 and Pentium D).

Distributed calculation system. The calculation jobs can be locally or remotely executed in transparent interactive mode. Windows and Unix systems can be mixed using encrypted TCP/IP connections.

Pentium optimized code and  586, 686, Pentium 4, K6, Athlon/Duron and Opteron/Athlon 64/Sempron 64 DLLs for maximum performances.