[gmx-users] Interaction study for peptide-receptor..

Justin Lemkul jalemkul at vt.edu
Thu Oct 4 16:21:41 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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