----- Original Message -----
From: TJ Mustard <musta...@onid.orst.edu>
Date: Tuesday, September 14, 2010 10:54
Subject: [gmx-users] FEP top file setup...
To: "gmx-users@gromacs.org" <gmx-users@gromacs.org>
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> I am tryng to run free energy perturbation (FEP) calculations on several
> ligands in several proteins. My problem is getting the correct B state atoms
> and charges for AMBER forcefields. If anyone can point me in the correct
> direction, that would be great.
I have read the Free Energy Tutorial from the Dill group wiki and found
it very informative on how I should set up the top file and the experiment as a
whole. But I can't seem to get the jobs to run correctly. I am assuming that
the top file is incorrectly setup as the jobs run with lambda = 0.
|
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It sounds to me more like your .mdp might be wrong. Check out the FE section
of manual 7.3
Mark
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