[gmx-users] membrane-protein simulation

Justin Lemkul jalemkul at vt.edu
Wed Aug 2 19:03:09 CEST 2017

On 8/2/17 5:01 AM, Amir Zeb wrote:
> Hello gmx-user
> I want to simulate a membrane protein with more than one chains like A, B,
> C etc. I generated the strong_posre.itp  file as Justing has kindly
> explained in his tutorial, and updated the topol.top file by inserting the
> same lines. I also updated the minim.mdp file by inserting STRONG_POSRES.
> Once I tried the minimization of the system before the shrinking step, I
> got the error as below:
> Fatal error:
> [ file strong_posre.itp, line 548 ]:
> Atom index (544) in position_restraints out of bounds (1-543).
> This probably means that you have inserted topology section
> "position_restraints"
> in a part belonging to a different molecule than you intended to.
> In that case move the "position_restraints" section to the right molecule.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> I tried so many options but could not fix the issue. Please keep in view
> that the same procedure is working well with a single chain of the protein.
> Kindly help me how to fix this issue?

You need to create restraint files for each chain separately and include them in 
each [moleculetype] separately, as explained here:




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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