[gmx-users] Problem with DMSO as solvent

Justin A. Lemkul jalemkul at vt.edu
Wed Jan 7 22:18:27 CET 2009

Suman Chakrabarty wrote:
> Hi,
> I tried to use DMSO as solvent and encountered the following problems:
> 1. genbox can generate the solvated box configuration alright, but it
> does not add the number of solvent molecules in the topology file. I
> need to add both the dmso.itp entry and the number of solvent molecules
> manually.
> Here is the last part of the genbox output:
> ==================================================================
> Generated solvent containing 103792 atoms in 25948 residues
> Writing generated configuration to solvated.gro
> Back Off! I just backed up solvated.gro to ./#solvated.gro.2#
> Giving Russians Opium May Alter Current Situation
> Output configuration contains 103892 atoms in 25949 residues
> Volume                 :     3038.27 (nm^3)
> Density                :     1108.66 (g/l)
> Number of SOL molecules:      0
> ===================================================================
> Is it expected behaviour? It would be rather nice to be able to select
> the solvent in the first step of creating the topology using pdb2gmx as
> well and if genbox could add the number by itself.

That is to be expected; you aren't adding SOL, are you?  A simple:

grep DMSO solvated.gro | wc -l

will do the trick.

> 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.


> 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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