[gmx-users] Values for pairs, when attached to the topology...?

Maik Goette mgoette at mpi-bpc.mpg.de
Fri May 13 14:49:01 CEST 2005

Hi all

I have a problem with parameters, manually included to the pairs 
section. For FEP purposes, I have(?) to include the pair parameters for 
the perturbed atoms ((A and B value) into the topology file (OPLSAA FF).

I took the values eps and sig for the two atoms i and j from the 
nonbonded topology, calculated the ij value via the formulas in the 
manual and inserted these values for eps and sig in the topology file.

mdrun claims, that the parameters are wrong:

Fatal error: Force field inconsistency: 1-4 interaction parameters for 
atoms 1615-1621 not the same as for other atoms with the same atom type

Obviously, the parameters, I calculated are wrong. Do I have to include 
fudge-factors in my calculations ?
I am also not sure, if there have to be c6 and c12 in the topology file, 
or if eps and sig are ok.

Please give me some information, how the parameters out of the 
forcefield have to be calculated correctly and which ones I have to use 
in my topology file


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

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