[gmx-users] Re: Simulation of a protein in a water/DMSO box

Simone Cirri simonecirri at gmail.com
Wed Sep 30 13:24:03 CEST 2009

Justin A. Lemkul wrote:

Simone Cirri wrote:
> Hi everyone,
> I need to run a simulation of a protein in a water/DMSO mixture. I can't
> quite understand how should I do this... should I normally solvate the
> protein with water and then replace a certain number of water molecules
> (according to the needed % of DMSO) with DMSO molecules? But in this case,
> how should I do it? Is there a way of replacing solvent molecules with other
> solvent molecules, but of a different type?
> I'm sorry but I don't know which procedure to follow.
> Thanks in advance
> The easiest way I can think of is to define the box around your protein,
> use genbox -ci -nmol to insert the desired number of DMSO molecules, and
> then fill the box with water. You may have to tweak the box size or use
> genbox -maxsol to get the desired concentration.

Hi Justin, I've tried your method. More or less, it works: I manage to
insert the exact desired number of DMSO molecules, and when I fill the box
with water, I get slightly less molecules that the ones I calculated, but I
think I can ignore that.
The problem comes with grompp, because I get the error:

Fatal error:
number of coordinates in coordinate file (1JIC_dmso_water.gro, 17314)
             does not match topology (1JIC.top, 16454)

because, evidently, the .top file does not contain any trace of the 215 DMSO
molecules I added (215 x 4 = 860, which is the difference of coordinates
between the .gro file and the .top file).
I tried to add a line:
#include "dmso.itp"
but I get another fatal error:

Fatal error:
Atomtype SD not found

due to the fact that I'm using the AMBER99 forcefield. In fact, this
forcefield (as I've seen in the .atp file) only contains 2 types of S:
S (sulphur in disulfide linkage)
SH (sulphur in cystine)
and I guess that none of them is the right one... so I don't think I can
simply rename the SD in the dmso.itp file to S, for example.
How should I solve the problem, then?
Thank you very much

Simone Cirri

simonecirri at gmail.com
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