[gmx-users] Generating solvent topology using pdb2gmx

Suman Chakrabarty suman at sscu.iisc.ernet.in
Mon Jul 13 05:10:03 CEST 2009


I am trying to generate the topology file for a system containing a single
polymer chain in pure DMSO. I have successfully generated the system
configuration using genbox. But when I run pdb2gmx on it to create the
topology file using the G53a6 force field, it treats the whole system as a
single molecule (both polymer and DMSO). Such that the [ molecules ] section
of the topology file contains:

[ molecules ]
; Compound        #mols
Protein             1

Is there any way to use pdb2gmx in a way such that it treats the solvent
molecules within separate moleculetype? Otherwise there is no direct way to
use the solvent parameters provided within the ffG53a6.rtp file.

Or should I manually create a dmso.itp file using the same parameter set? It
seems the G53a6 force field has rather different parameter set as compared
to the supplied dmso.itp file containing ffgmx parameters. Is it advisable
to use the supplied dmso.itp file within the G53a6 force field?

Best regards,
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