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

Jackson Chief jchiefelk at gmail.com
Mon Mar 26 07:13:39 CEST 2012

The missing residues correspond to a loop that connects two alpha helices.
 The C-terminal end of one helix, and N-terminal end of the other helix
contain a random coil.  After energy minimization, the coils are extended
in space and not connected.  I visualized this by looking at the .gro file
in VMD.  After 5ns of unrestrained MD, the two coils are clearly connected
by looking at the output .gro file in VMD.  Weird.

On Sun, Mar 25, 2012 at 9:48 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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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