Suman Chakrabarty wrote:
Hi,
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
field?
On general principles, don't mix force fields. Search the archives of
this list and/or literature for discussion of DMSO parameters.
Mark
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