AMBER Archive (2008)

Subject: Re: AMBER: Nmode - entropy calculation of receptor - should I apply restraint?

From: David A. Case (case_at_scripps.edu)
Date: Thu Jun 05 2008 - 13:50:16 CDT

On Thu, Jun 05, 2008, Seth Lilavivat wrote:
>
> If I calculating entropy using nmode of ligand-receptor complex, should I
> apply restraints when I am running nmode on the receptor so that the cavity
> or binding site does not move very much during minimization? It seems like
> minimizing the receptor alone without restraints would result in large
> movement of the structure and skew the results.

You should try it (without restraints) and see. In most cases, minimization
is pretty local, and doesn't lead to large-scale distortions of the structure.
Adding in restraints were certainly complicate the analysis.

...dac

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