[gmx-users] pdb2gmx for non-proteins

Christoph Freudenberger christoph.freudenberger at chemie.uni-ulm.de
Tue Apr 15 19:01:01 CEST 2003

Hi there,

I'm thinking about how to generate the top's for tripodal
scaffold-molecules bearing different substituents:


The scaffold is an aryl-ring and R1-3 should be arbituary
I wonder if it is possible to add rtp-entries for Scaf and
the R's and let pdb2gmx do the job.
Is pdb2gmx able to handle non-chain-like molecules?
How are the links recognized? Automaticly (e.g. by distance)
or do I have to define them?
Is it vital to have the atoms in the same sequence in the
pdb and the rtp?

Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785

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