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

Mark Abraham Mark.Abraham at anu.edu.au
Mon Mar 26 05:48:41 CEST 2012

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.


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