[gmx-users] Generating solvent topology using pdb2gmx
Mark.Abraham at anu.edu.au
Mon Jul 13 05:26:28 CEST 2009
Suman Chakrabarty wrote:
> 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?
No... pdb2gmx only writes one [moleculetype], IIRC.
> Otherwise there is no direct way
> to use the solvent parameters provided within the ffG53a6.rtp file.
I recommend using pdb2gmx on a coordinate file with only polymer to
generate a basic .top file, and only then apply genbox to generate a
solvated version of that coordinate file. Then you edit the .top file to
change [molecules] appropriately and #include a suitable dmso.itp file
at the right place. Now you have a solvated polymer and a corresponding
.top file for inputs to grompp.
> 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
On general principles, don't mix force fields. Search the archives of
this list and/or literature for discussion of DMSO parameters.
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