[gmx-users] Problem with DMSO as solvent

[Suman Chakrabarty]

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.

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?


Thanks and regards,
Suman Chakrabarty.