[gmx-users] Problem with DMSO as solvent

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 8 00:12:52 CET 2009

Suman Chakrabarty wrote:
> On Thu, Jan 8, 2009 at 2:48 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>> 2. grompp with the modified topology file returns the following error:
>>> -------------------------------------------------------
>>> Program grompp, VERSION 4.0.2
>>> Source code file: ../../../SRC/src/kernel/toppush.c, line: 897
>>> Fatal error:
>>> Atomtype SD not found
>>> -------------------------------------------------------
>>> On searching mailing list archive, I found that there is problem with
>>> the dmso.itp file:
>>> http://www.mail-archive.com/gmx-users@gromacs.org/msg15431.html
>>> It seems the "mass" column is missing in dmso.itp even in the latest
>>> version of Gromacs. Is there any corrected version of this file
>>> available? Or do I need to manually put these values? It would be nice
>>> if this file is corrected in some later version.
>> I think the problem is mixing of force fields.  The dmso.itp included in
>> /share/top is based on ffgmx.  Are you using ffgmx?  If so, don't.  If you
>> are using another force field, then you will need to completely update
>> dmso.itp to correspond to the new parameters.  Excellent DMSO parameters
>> exist under Gromos96 53a6, IIRC.
>> The mass column is needed, but is not the cause of your specific problem.
> Thanks for your response Justin. I am using the GROMOS96 43a2 force
> field. I shall try to modify the dmso.itp and dmso.gro accordingly and
> see what happens.

If you can find 43a2 parameters for DMSO, sure.  But the best model so far (that 
I know of) is:


> A newbie question: what is the right way to search for existing DMSO
> parameters under any given force field, e.g. Gromos96 53a6 as you
> mentioned?

Google, Pubmed, SciFinder, Web of Science, etc. are my common methods (you would 
find the paper I linked above in just a few minutes).


> Thanks and regards,
> Suman Chakrabarty.


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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