[gmx-users] Generating solvent topology using pdb2gmx

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jul 13 05:26:28 CEST 2009

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.


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