AMBER Archive (2003)

Subject: AMBER: Gibbs pmf calculation

From: Lishan Yao (yaolisha_at_pilot.msu.edu)
Date: Fri Aug 15 2003 - 10:35:51 CDT


Hi:
   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
distance?
Thanks in advance.

Best,
Lishan
   

-- 
Lishan Yao <yaolisha_at_pilot.msu.edu>
MSU

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