1. Introduction
VEGA was developed to create a bridge between most of the molecular software packages, like BioDock, Quanta/CHARMm, Insight II, Mopac, etc. In this tool have been also implemented some features that are useful to analyze, display and manage the 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 PCs, Linux, FreeBSD, NetBSD, AmigaOS, etc.
The most important features implemented in VEGA are:
Supported input file formats: Alchemy, Accelrys Insight .car and .arc, Accelrys Quanta/CHARMm CRD, CSR, MSF and DCD, BioDock output, Cambridge Data File (CSSR), Chem3D, Cartesian coordinates (XYZ), ESCHER NG solutions, GAMESS cartesian input and output, Gromos/Gromacs .gro and .xtc, HyperChem .hin, Interchange File Format (IFF), QMC, MDL Molfile, Mopac internal coordinates, Protein Data Bank (PDB), Data Bank with ATDL atom types (PDBA), Protein Data Bank Fat (PDBF), Protein Data Bank MultiModel, Tripos Sybyl (Mol2).
Supported output file formats: Accelrys Insight .car (archive 1 and 3), Accelrys Quanta/CHARMm CRD and MSF, Alchemy, Cambridge Data File (CSSR), Cartesian coordinates (XYZ), Fasta, GAMESS cartesian, Gromos/Gromacs .gro, Interchange File Format (IFF), MDL Molfile, 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 simplified, Tripos Sybyl (Mol2), VRML.
Supported surface formats: CSV, IFF, Insight, Quanta, raw binary, VRML.
Multiple files load for assemblies creation.
Atomic charge attribution with Gasteiger method or through a template of residues.
Atom type attribution for AMBER, Bond, Broto/Moreau, CHARMm, CHARMM 22 for nucleic acids, CHARMM 22 for lipids, CHARMM 22 for proteins, CFF91, CVFF, Ghoose/Crippen, GRID, H-bond, Meng, MM+, MM2, MM3, Tripos, UNIV and any other user defined template. A simple language to define the atom types is built-in (ATDL).
Calculation of molecular surface (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 (CVFF force field only) for each residue involved in the binding.
Evaluation of logP (Broto/Moreau, Ghoose/Crippen, Virtual logP*) and lipole (Broto/Moreau, Ghoose/Crippen).
Dynamic trajectory analysis with the support for Accelrys archive file (.arc), BioDock output, CSR (Accelrys conformational search), DCD, ESCHER NG, Gromacs .xtc and PDB multimodel 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*.
Coordinates normalization.
Molecule solvatation with any type of cluster.
Deletion of water molecules and hydrogen atoms.
Residue renumbering.
* Implemented only in full version of VEGA package.