[gmx-users] two peptides in simulation tend to stick together
refmac5 at gmail.com
Fri Apr 20 16:28:05 CEST 2018
Thank you Justin!
On Sun, Apr 15, 2018 at 10:48 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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
>> and they are both named chain A. However after the simulation I found
>> 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
> 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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