[gmx-users] Interaction study for peptide-receptor..
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
> 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
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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