[gmx-users] How to get the all atom topology file for smallmolecule?

[Dr. Christoph Freudenberger]

Peter Zoon wrote:
> But doesn't pdb2gmx only work is there are valid amino-acid residue 
> types specified in your pdb-file? If this is a small drug molecule I can 
> imagine that it isn't made from amino-acids.

No, pdb2gmx works with any kind of molecule, "all" you need to assign
are atom types, a bond topology and some improper dihedrals. For
most small molecules this can be easiely done by hand. You
can even build oligo/polymeric structures form small building blocks
using the specbonds file.

regards
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Dr. Christoph Freudenberger
Institut fuer Organische Chemie and Biochemie II
Technische Universitaet Muenchen
Lichtenbergstr. 4
D-85747 Garching, Germany

Tel.: ++49 (0)89 289 13313
Fax.: ++49 (0)89 289 13210
email: Christoph.Freudenberger at ch.tum.de
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