[gmx-users] Problem Simulating a protein with small peptides

Justin Lemkul jalemkul at vt.edu
Thu Dec 18 13:47:15 CET 2014

On 12/18/14 7:21 AM, Arash Firouzbakht wrote:
> Dear GROMACS experts,
> I am simulating a protein with a number of KVV tripeptides, using run
> parameter files in GROMACS tutorial website(Dr. Justin Lemkul) with
> changing JZ4 to KVV and changing temperature to 310K.
> After I add the KVV coordinate file(KVV.gro, attached) to the protein box
> and further solvate it, the output .gro file seems to be OK. But once I
> subject it to the genion command to neutralize the charge the output
> coordinate file changes ! All KVV residues change to their subresidual
> names which are recognized by the software as LYS-VAL-VAL. I need GROMACS
> to recognize the tripeptides with their former name.
> I attached part of the problematic .gro file containing KVV coordinates.

The list does not accept attachments.

> How can I solve this issue?

Don't approach this problem as in the tutorial.  pdb2gmx can handle multiple 
protein chains natively.  There is no need to treat a peptide ligand as you 
would some xenobiotic.  Just pass the protein-peptide complex to pdb2gmx and it 
will set up the topology for you, provided you have suitable TER delimiters or 
chain identifiers.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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