Automated Topology Builder

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Automated Force Field Topology Builder (ATB) and Repository for the GROMOS family of force fields

The ATB and Repository is intended to facilitate the development of molecular force fields for Molecular Dynamics or Monte Carlo simulations of biomolecular systems. Applications include:

   * The study of biomolecule:ligand complexes
   * Free energy calculations
   * Structure-based drug design
   * The refinement of x-ray crystal complexes

This site provides:

   * A repository for building blocks and interaction parameter files for molecules described using GROMOS force fields.
   * An automated builder to help generate building blocks for novel molecules, compatible with the GROMOS 53A6 force field 
     and in formats appropriate for the GROMACS, GROMOS and CNS simulation packages.
   * Refined geometries for molecules within the repository.
   * Equilibrated starting coordinates for a range of biologically important systems.

Required Input:

   * A coordinate file in Protein Data Bank (PDB) format (including all hydrogen atoms).
   * A connectivity record in PDB format listing all interatomic bonds.
   * The net charge on the molecule.

Output Provided:

   * Building block files (all atom and united atom).
   * Interaction parameter files for the corresponding force field.
   * Optimized geometries (all atom and united atom).

The building block and interaction parameter files are provided in a range of formats that can be used to generate the appropriate topology files.

Disclaimer: While all effort has been made to provide appropriate estimates of the parameters including where appropriate alternative choices the user should carefully examine all files before use.

A detailed description of methodology used by the automated topology builder is given here. A detailed description of the software implementation is found here.

GROMOS home page is found here.

An introduction to the GROMOS force field is given here.

The compbio homepage is here.