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

[Mark Abraham]

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