[gmx-users] Problem with DMSO as solvent

Suman Chakrabarty suman at sscu.iisc.ernet.in
Wed Jan 7 22:08:19 CET 2009


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

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.

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:

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.

Suman Chakrabarty.

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