AMBER Archive (2009)

Subject: Re: [AMBER] chain restrain x TI

From: David A. Case (
Date: Thu Apr 30 2009 - 13:01:13 CDT

On Wed, Apr 29, 2009, Josmar R. da Rocha wrote:
> I'm trying set up a MD simulation of protein-ligand-cofactor
> complex. The protein I'm working is a homotetramer, however, the focus
> of the analysis is only on one of then,  where I modeled a ligand using
> molecular docking. In order to speed up the MD simulation I thought
> of restraining that only to that the monomer containing the ligand.

Does it make sense to only include the monomer with the ligand? An
alternative would be to use restraints on the other three monomers (say with
a restraint weight of something like 1.0 kcal/mol-A^2). Of course, that
doesn't speed up the calculation, but neither does using a belly. In Amber,
if you don't actually get rid of some parts of the system, you essentially
have to pay for simulating all of it.

..hope this helps...dac

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