AMBER: Gibbs pmf calculation

From: Lishan Yao <>
Date: 15 Aug 2003 11:35:51 -0400

   I want to use Gibbs PMF method (umbrella sampling) to pull out the
ligand from active site to calculate binding free energy. I need a
distance restraint. But when I look at the Manual, I find out nmropt
belongs to sander. What should I do? Another question is since I don't
change any paremeters, can I just make prmtop & inpcrd files just the
same way as I did for sander MD simulation? Then how can I define the
change of lembda is corresponding to the change of ligand protein
Thanks in advance.

Lishan Yao <>
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Received on Fri Aug 15 2003 - 16:53:01 PDT
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