Hope you will perform conformational search by production trajectory
run without any restraints. Preliminary equilibration stages is just
for equilibration of the starting system).
On Wed, Mar 16, 2011 at 5:37 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi everybody,
>
> I've been running simulations involving ligand-receptor complexes and found that my ligand does not explore the complete conformational space of the binding pocket.
>
> I have applied weak restraints on the complex by analogy to tutorial 3, that is restraint_wt=2.0 (http://ambermd.org/tutorials/advanced/tutorial3/section1.htm). The restraints was applied both on the protein residues and the ligand during both density and pressure equilibration. My question is whether removing the restraints on the ligand during pressure equilibration would result in a more effective search of conformational space.
>
> Thanks in advance for any suggestions on the matter.
>
> Regards
>
> George
>
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--
Dmitry Nilov,
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
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Received on Wed Mar 16 2011 - 08:30:04 PDT
