Ok I think I know where you are going with this.
I started a small 2 nucleic acid system. I set RNA_Chain_A as the couple-moltype and couple-lambda0 and couple-lambda1 to vdw-q and none respectively. I then began a steep mdrun and got this error:
Program mdrun, VERSION 4.5
Source code file: topsort.c, line: 112
Fatal error:
Function type Improper Dih. not implemented in ip_pert
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
I have searched for this on google and found nothing. Do I need an Improper Dihedral section in my top/itp file?
Any help is much appreciated.
----- 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>
> 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
Mark
TJ Mustard
Email: musta...@onid.orst.edu
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