[gmx-users] grompp is adding a bond in my model that should not be there

Jackson Chief jchiefelk at gmail.com
Mon Mar 26 03:20:55 CEST 2012

I made a model of a receptor protein, bilayer, and solvent.  My protein
contains a 20 residue gap.  This gap corresponds to a region of the protein
that had been digested by trypsin before crystallization.  The trypsin
digestion has no affect on receptor activity experimentally. I performed
energy minimization without problem.  The protein looked like it should,
containing the gap.

When I performed equilibration, the output had the C-terminus of one
protein fragment connected to the N-terminus of the other protein fragment.
 I don't know how this peptide bond was created, because it was not in the
input *.gro file to grompp.  Please help.

Jackson Chief Elk
Graduate Student in Biophysics and Biochemistry
The University of Montana
Missoula, MT
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