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.