[gmx-users] two peptides in simulation tend to stick together

Justin Lemkul jalemkul at vt.edu
Sun Apr 15 16:49:02 CEST 2018

On 4/12/18 10:57 PM, MD wrote:
> Hi Gromacs folks,
> I was trying a simulation to look at a protein (35kDa) and a peptide (10
> amino acids)interaction. I prepped one pdb file containing both the protein
> and the peptide. The original position of the peptide is in a hydrophobic
> pocket of the protein from a docking result. I used 1-10 to number the
> peptide and I kept the original protein numbering system (23-336) as it is,
> and they are both named chain A. However after the simulation I found quite
> some structures have the #10 of the peptide trying to get close to #23 of
> the protein. I used the tutorial mdp file and the protein and peptide are
> easy to start with (no modified residues). I wonder if I am missing some
> parameters setting up at the starting point? Or by simply naming them with
> different chain names will fix the problem?

If they had the same chain identifier, pdb2gmx may have written the 
topology as a single polypeptide chain. You need to check and make sure 
you actually have two separate topologies reflecting two separate 
peptides. This is done either with a TER delimiter or a change in the 
chain identifier.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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