[gmx-users] error in grompp

[Justin A. Lemkul]

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
> "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.
>
>
> 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].

http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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