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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