[gmx-users] FEP top file setup...

Mark Abraham mark.abraham at anu.edu.au
Tue Sep 14 04:24:01 CEST 2010

----- Original Message -----
From: TJ Mustard <mustardt at onid.orst.edu>
Date: Tuesday, September 14, 2010 10:54
Subject: [gmx-users] FEP top file setup...
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>


> 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.

It sounds to me more like your  .mdp might be wrong. Check out the FE section of manual 7.3


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