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.
-Justin
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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