[gmx-users] error in grompp

reisingere at rostlab.informatik.tu-muenchen.de reisingere at rostlab.informatik.tu-muenchen.de
Sat Jul 7 14:20:08 CEST 2012

Hi everybody,
I want do to an energy minimization and simulation with position restraints.
Additionally to the protein I have a membrane around my protein which I
also ant to fix. If I won't fix it, it is in the whole box after the
minimization and simulation but not around my protein.
Since I only want the hydrogen atoms to be flexible I use the second
option "protein-h" when I was asked by genrestr. This makes that the whole
protein including the membrane of dummy atoms is fix.
But when I want to use grompp I get the error:

Atom index (4942) in position_restraints out of bounds (1-4941).
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.

The first 4941 atoms are of the "real" protein without the membrane and
after this the membrane starts:

 313LEU    OC1 4940   3.429   4.330   3.090
  313LEU    OC2 4941   3.337   4.305   3.259
  314DUM    DUM 4942   1.996   2.371   6.171
  315DUM    DUM 4943   1.996   2.371   6.271
  316DUM    DUM 4944   1.996   2.471   6.171

When I remove the restriction of the DUM atoms I don't get the error but
that is not what I want.

Can you please tell me how I can fix the membrane?

Thank you,

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