Simone Cirri wrote:
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).
Right, because you need to add these molecules to the [molecules] directive in
your .top.
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?
The dmso.itp file is for use with the deprecated ffgmx force field. There are
good parameters in the literature for Gromos96 53a6, and perhaps others. You
will have to find suitable parameters for DMSO that are compatible with Amber99.
They may exist somewhere, but if not, you have to derive them yourself, which
is not an easy task.
-Justin
Thank you very much
Simone Cirri
[email protected] <mailto:[email protected]>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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