AMBER: how to use independently

From: Jufang Shan <>
Date: Mon, 12 Apr 2004 21:23:36 -0500


I want to calculate the binding free energy between receptor and ligand. I calculated the entropy for the complex, receptor and ligand using normal mode separately since the same parameters don't work for all. My question is what value shall I give to "calc delta" (?0..1) and "calc decomp" (?0..2) to run I am using Amber 7.


Jufang Shan
Graduate Student
Dept. of Structural Biology
St. Jude Children's Research Hospital
Interdisciplinary Program
The University of Tenessee Health Science Center
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Received on Tue Apr 13 2004 - 03:53:00 PDT
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