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 PCs, Linux, FreeBSD, NetBSD, AmigaOS, etc.
The most important features implemented in VEGA are:
- Supported input file formats: MSI Quanta/CHARMm CRD and DCD, Cambridge Data File (CSSR),
QMC, GAMESS cartesian, Gromos, HyperChem (HIN), Interchange File Format (IFF), Tripos
Sybyl (Mol2), MDL Mol, MSI Quanta MSF, Protein Data Bank (PDB), Protein Data Bank Fat
(PDBF), MSI/Biosym Insight II (.car), MoPac internal coordinates, cartesian coordinates
(XYZ).
- Supported output file formats: MSI Quanta/CHARMm CRD, Cambridge Data File (CSSR), Fasta,
GAMESS cartesian, Gromos, Interchange File Format (IFF), Tripos Sybyl (Mol2), MSI Quanta
MSF, Protein Data Bank (PDB), Protein Data Bank with atomic charges (PDBQ), Protein Data
Bank Fat (PDBF), Protein Data Bank simplified, MSI/Biosym .car (old and new), MoPac
internal coordinates, MSI/Biosym surface, MSI Quanta surface, VRML, cartesian coordinates
(XYZ).
- Multiple files load for assemblies creation.
- Atomic charge attribution with Gasteiger method or through a template of residues.
- Force field attribution for AMBER, CHARMm, CVFF, MENG, 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)*).
- Calculation of ligand-receptor interaction energy (only with CVFF force field) for each
residue involved in the binding.