[gmx-users] membrane-protein simulation

[Amir Zeb]

Thanks Justin

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
>> "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:
>
> http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_
> position_restraints_out_of_bounds
>
> -Justin
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
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