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| Automated Force Field Topology Builder (ATB) and Repository for the GROMOS family of force fields http://compbio.biosci.uq.edu.au/atb/
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| 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:
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| * The study of biomolecule:ligand complexes
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| * Free energy calculations
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| * Structure-based drug design
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| * The refinement of x-ray crystal complexes
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| This site provides:
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| * A repository for building blocks and interaction parameter files for molecules described using GROMOS force fields.
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| * 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.
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| * Refined geometries for molecules within the repository.
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| * Equilibrated starting coordinates for a range of biologically important systems.
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| Required Input:
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| * A coordinate file in Protein Data Bank (PDB) format (including all hydrogen atoms).
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| * A connectivity record in PDB format listing all interatomic bonds.
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| * The net charge on the molecule.
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| Output Provided:
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| * Building block files (all atom and united atom).
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| * Interaction parameter files for the corresponding force field.
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| * Optimized geometries (all atom and united atom).
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| The building block and interaction parameter files are provided in a range of formats that can be used to generate the appropriate topology files.
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| 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.
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| A detailed description of methodology used by the automated topology builder is given here. A detailed description of the software implementation is found here.
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| GROMOS home page is found here.
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| An introduction to the GROMOS force field is given here.
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| The compbio homepage is here.
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