[gmx-users] Re: gmx-users Digest, Vol 77, Issue 138
lloyd.riggs at gmx.ch
Wed Sep 22 20:45:16 CEST 2010
I'm not sure if this is a bug or not. I downloaded and installed the new version of Gromacs, and compiled it fine, and recompiled just mdrun_mpi....
The problem I now encounter. U was using 53a6 FF, which worked in the past, although I am partial to all atoms. In Pro residues, the topolog output from grompp lables three of the CH2 in the ring as CH2r. When I then do an EM or MD, gromacs complains that it can not find atom type CH2r. I looked through all the .itp, .rtp and amino acid definitions, and CH2r is there. If I re-lable the topology and .gro file by hand to CHR1 the system works, but the overall geometry is slightly off (if you look at the atom definitions and take into account that prolines are not completly aeromatic, only partially...
In any case, is this a bug or is there some other problem I missed? I did look at the input .pdb file, and the same nomenclature I used before with the same ff now does not work?
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