On 26/03/2012 12:20 PM, Jackson Chief wrote:
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.
You have to treat this gap somehow. Either you have to cap the peptide
chains (see pdb2gmx -h), or model in the missing residues using some
(non-GROMACS) software.
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.
.gro files have coordinates, never bonds. Since you haven't described
how you are treating the gap, and haven't said how you've observed the
"creation" of a peptide bond, it's hard to give specific guidance.
Mark
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