[AMBER] General question on applying restraints during production MD

From: George Tzotzos <gtzotzos.me.com>
Date: Tue, 26 Jan 2016 11:16:26 +0100

My system consists of a homodimer receptor and two identical ligands, one in each subunit of the receptor. The receptor also consists of one water molecule per subunit. The latter are assumed to be conserved. The system was minimised, heated and equilibrated applying constraints on the complex (restraint_wt = 2.0). The receptor waters form H-bonds with receptor residues and the ligand and are in proximity of the dimer interface.

I’m currently conducting a 100 ns production MD in which the restraints have been removed. My goal is to determine whether the ligands have an effect in the formation of the homodimer interface, so I want to have a reasonable estimate of the relative binding of the two subunits in the presence and absence of the ligands.

The water of one of the subunits dissociates from the receptor after ~25 ns. The 2nd water molecule did not dissociate from the receptor.

My question is whether it is legitimate to repeat the production MD maintaining the constraints on the water molecule but not on the rest of the system.

Thanks in advance for any suggestions



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Received on Tue Jan 26 2016 - 02:30:04 PST
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