On 7/16/12 5:36 AM, Raj wrote:
Hi all,
It may be naive but I would like to get some clear explanation in SMD ( COM
pulling) reg. The question is, Before performing the COM-pulling (incase of
protein ligand complex) do we need to position restrain the ligand using
genrestr and then add the topology to the topol.top file. If not why should
not we restrain the ligand. Thanks in advance
The initial equilibration can be approached in a number of ways that includes
restraining both the protein and ligand or one or the other. Restraints are
only intended to avoid large structural changes due to reorganization of the
solvent. Thus you may choose to restrain the whole complex initially and then
reduce or remove the restraints over the course of further equilibration. There
are no hard and fast rules. Look into the literature and see what others
recommend, and evaluate for yourself whether or not such a protocol is
reasonable in your case.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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