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#50 Gromacs Topology Files

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open
Tim Vandermeersch
Output (10)
5
2012-10-23
2006-10-24
Anonymous
No

From: fparnold@binghamton.edu

Gromacs provides several force-fields for use in simulation, including
OPLSAA and the Amber FF used by the Folding@Home group.

In order to simulate an organic molecule using Gromacs, a topology
file, which includes atom types and charges, bond-pairs, estimated
bonding parameters, angles, dihedrals, etc., must be constructed as
well.

There are two tools currently available: x2top, which is part of the
Gromacs distribution, but which contains little chemical intuition, and
the Dundee PRODRG server, which generates united-atom (i.e. non-
polar hydrogens are not included) structures only.

Therefore, the request would be for OpenBabel to use its atom-typing
abilities to assign, even approximate, atom-types to a structure, then
generate the rest of the bond, dihedral, etc, interactions. Atom types
and charges could be manually corrected by the researcher for a given
topology (and will probably have to be), but as force-constants are
similar for similar bonds, the rest of the file should be usable as-is.
The output could use either the formal Gromacs files, or create atom-
types of ob_???, where ??? would be sp2 carbon, carbonyl oxygen,
aromatic carbon, etc, and ob would identify these types as OpenBabel
atom-types, using some idealized gromacs bonding parameters.

Files and descriptions may be found at
http://www.gromacs.org/contributed_by_users/task,cat_view/gid,36/

and the manual in HTML form at
http://www.gromacs.org/gromacs/documentation/paper-
manuals.html

An example is attached.

Discussion

  • Nobody/Anonymous

    Nobody/Anonymous - 2006-10-24

    Gromacs Toplogy File

     
    napthalene.top

  • Geoff Hutchison

    Geoff Hutchison - 2008-05-27

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    I believe Tim has handled this for .xtc files, correct Tim? If so, let's close this.

     

  • Tim Vandermeersch

    Tim Vandermeersch - 2008-05-27

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    xtc files are used as output while the topology files (.top) are input. The problem with gromacs is that it's hard to assign the correct types and parameters for molecules other than amino acids, DNA bases, ...

    So this is more like a feature request to have an input generator like we have for GAMESS in Avogadro.