[gmx-users] membrane-protein simulation
zebamir85 at gmail.com
Thu Aug 3 04:18:49 CEST 2017
Got it, it's working.
On Wed, Aug 2, 2017 at 10:02 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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
>> 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
>> 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
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users