[gmx-users] membrane-protein simulation

Amir Zeb zebamir85 at gmail.com
Wed Aug 2 11:01:54 CEST 2017

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 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?

Thanks in advance

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