[AMBER] Restraints on equilibration of solvated complexes

From: George Tzotzos <gtzotzos.me.com>
Date: Wed, 16 Mar 2011 15:37:17 +0100

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.



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Received on Wed Mar 16 2011 - 08:00:04 PDT
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