Subject: Announcing VEGA 1.1 Final Release

From: "Giulio Vistoli" <[email-masked]>
Date: Mon, 3 Apr 2000 11:44:46 +0200

Dear CCLers,
we are glad to announce that the final 1.1 release of VEGA package is now
ready for free download on our web server (http://users.unimi.it/~ddl).

VEGA was developed to create a bridge between most of the molecular software
packages, like Quanta/CHARMm, Insight II, MoPac, BioDock, 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, 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, Gromos, Interchange File Format (IFF), Tripos Sybyl
(Mol2), 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, 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 and any other user
defined template. A simple language to define the atom types is built-in.
- Calculation of molecular surface (Van der Waals, accessible to solvent and
Molecular Electrostatic Potential).

- Calculation of ligand-receptor interaction energy (only with CVFF force
field) 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 (interatomic distance, angle, torsion, angle
between two planes, molecular surface, surface diameter, molecular volume,
volume diameter, dipole, 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.

Thank you for your attention.

        Giulio Vistoli & Alessandro Pedretti

--
Ist. di Chimica Farmaceutica e Tossicologica
Viale Abruzzi, 42
I-20131 Milano (Italy)
Tel. +39-02-29502230
Fax +39-02-29514197
E-Mail: [email-masked]
WWW: http://users.unimi.it/~ddl