AMBER Archive (2008)

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

From: Seth Lilavivat (
Date: Thu Jun 05 2008 - 12:03:08 CDT

Dear Amber users,

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.


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