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

Justin Lemkul jalemkul at vt.edu
Thu Oct 4 14:16:47 CEST 2012

On 10/4/12 8:08 AM, rama david wrote:
> Hi francesco,
> Thank you For reply.
> I did docking but the result are not so impressive.
> I used vina and autodock.
> I also did virtual screening in autodock but the result are not upto the
> mark.
> Is the freezing of group can affect my system?? How much efficiency I get
> by these work??

You will not get any improvement in computational efficiency, and if you use 
NPT, you will get artifacts.  One can potentially speed up a calculation using 
energygrp_excl, but that's layering assumptions upon assumptions, which I think 
is bad news.  You've said you don't know if long-range interactions play a role. 
  That, to me, means you absolutely cannot justify any sort of freezing.

The fact that docking did not produce very good results is unsurprising.  The 
largely rigid treatment of proteins in docking leaves much to be desired.  This 
is yet another argument against freezing parts of your protein - if docking did 
not produce good results, why would you expect a mostly frozen MD system to 
perform much better?

> As these group are going to freeze in four simulation so if it affect one
> ligand it  affect other
> ligand also.
> I read article that did the work like me ,
> they sliced the binding residues and  used the inert solid sphere to
> support binding residues
> instead of the freezing group other group.
> I think both way should have same effect..Am I right or wrong??

I don't really understand what it is the other group did, aside from perhaps 
modeling a subsystem.  Still, I don't think such lengths are necessary or 
inherently beneficial.

> If you have any other way please suggest it..

I see no reason not to treat this system with normal MD protocols.



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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