On 10/4/12 2:01 AM, rama david wrote:
Hi gromacs Friends,
I want to do peptide-receptor ( Protein) interaction
study.Receptor consist a single chain.
Peptide is made up of 4 amino acids. I know the interaction pattern of
peptide and receptor.
I plan to mutate single residue each at a time and run 4 simulation .
So I will have the 4 different simulation that contain the mutated residues
and the wild one.
Then afterward from the interaction energy I want to select the peptide
which is showing
stronger interaction than others.
As mention I know the binding site, If I freeze the remaining portion in
receptor
that not involved in binding , Is it going to affect my screening process
???
Potentially. Do you know that the binding interactions and the mutations will
only perturb local residues? Do you know that there are no long-range motions
to be considered?
I think you gain very little by freezing portions of the system, and risk more
than you gain.
-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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