On 10/4/12 9:16 AM, rama david wrote:
Thank you for reply,
I read the recently published article in Biochemistry.
They worked on the same receptor that I am working.
( as I mention in my previous mail)
They used NAMD software and I am using gromacs.
They sliced the receptor binding site and used the the solid support
to the binding site and did simulation.
So if I freeze the group is it will ok ??
I've already stated my opinion on this matter, so I won't state it again.
I will not try to pre-judge a study I have not read (regarding the solid
support) but it seems to me that if you are analyzing the binding of a peptide
to a protein, that is fairly straightforward MD without anything fancy.
Is it possible in gromacs to fix the residue on solid immobilized surface.
If it is how to do it??
Build a surface, create a merged moleculetype, and define bonds between protein
atoms and surface atoms. This all sounds like a ridiculous amount of work.
my question is How to decide which group are remove and which group should
keep in simulation.????
IMHO, it's not worth doing in this way.
-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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