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.pilot.msu.edu>
MSU
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Aug 15 2003 - 16:53:01 PDT
