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

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Mar 26 07:17:06 CEST 2012


The problem is likely that pdb2gmx created the bond. It will have given a
long bond warning. You can add a ter statement in the pdb file at the break.



On Mar 26, 2012 5:49 AM, "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 ...
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 connecte...
.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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