[gmx-users] error in grompp
Justin A. Lemkul
jalemkul at vt.edu
Sat Jul 7 16:56:31 CEST 2012
On 7/7/12 8:20 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> 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?
You need a separate position restraint .itp file. As the error message states,
position restraints are only applicable per [moleculetype].
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users