[gmx-users] Problem with DMSO as solvent

Suman Chakrabarty suman at sscu.iisc.ernet.in
Thu Jan 8 01:12:45 CET 2009

On Thu, Jan 8, 2009 at 4:42 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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:
> dx.doi.org/10.1021/jp035034i

Thank you very much for this reference. I'll take it up right away.

But regarding 43a2 force field, I found the following entry in the
ffG43a2.rtp file. So I guess these are the required parameters for
DMSO. But in any case I'll be using the parameters given in the van
Gunsteren's paper.

[ DMSO ]
 [ atoms ]
SDmso SDMSO     0.13900     0
ODmso ODMSO    -0.45900     0
CDms1 CDMSO     0.16000     0
CDms2 CDMSO     0.16000     0
 [ bonds ]
SDmso ODmso    gb_38
SDmso CDms1    gb_39
SDmso CDms2    gb_39
ODmso CDms1    gb_44
ODmso CDms2    gb_44
CDms1 CDms2    gb_45
 [ angles ]
;  ai    aj    ak   gromos type
 [ impropers ]
;  ai    aj    ak    al   gromos type
 [ dihedrals ]
;  ai    aj    ak    al   gromos type

Thanks and regards,
Suman Chakrabarty.

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