Vega ZZ

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 significant features implemented in VEGA are:

  • Supported input file formats: Alchemy, AMMP, Accelrys Insight .car and .arc, Accelrys Quanta/CHARMm CRD, CSR, MSF and DCD, CML 1.0 and 2.0, BioDock output, Cambridge Data File (CSSR), Chem3D, ChemSol, Cartesian coordinates (XYZ), CPMD XYZ, ESCHER NG solutions, GAMESS cartesian input and output, Gaussian cartesian input and output,  Gromos/Gromacs .gro and .xtc, HyperChem .hin, Interchange File Format (IFF/RIFF), IUCr Crystallographic Information Framework (CIF, mmCIF), IUMSC CRT, QMC, MDL Molfile, Mopac cartesian coordinates, Mopac internal coordinates, Protein Data Bank (PDB), Data Bank with ATDL atom types (PDBA), Protein Data Bank Fat (PDBF), PQR, PQR XML, Protein Data Bank MultiModel, 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, 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, Interchange File Format (IFF), IUCr Crystallographic Information Framework (CIF), IUMSC CRT, MDL Molfile, 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 with more than 99999 atoms (PDBL), Protein Data Bank simplified, PQR, PQR XML, Tripos Sybyl (Mol2), VRML.
  • Supported surface formats: CSV,  IFF/RIFF, 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 TRR, Gromos XTC, IFF/RIFF (32 and 64 bit), Crystallographic Information Framework multi-model (CIF, mmCIF), MDL Mol multi-model, Tripos Mol2 multi-model and PDB 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.
  • Dynamic trajectory conversion with cut/skip frame and atom remove capabilities (VEGA ZZ only).
  • Coordinates normalization.
  • Molecule solvatation with any type of cluster.
  • Deletion of water molecules and hydrogen atoms.
  • Residue renumbering.

    Go to Vega ZZ  sites

 

 

 

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