[gmx-users] position restraints on backbone: index error

[Quyen Vu]

Hi,
Position restraints are per molecule.
if you separate your molecule like that, the position restraints of
backbone should be generated for each chain base on indices of each chain
and include it in the topology of the chain, not global topology like that.
so for example, if you want restraint backbone of chain E, you have to
generate position restraint base on the topology of chain E and include him
in 2bnr_SLLDWITQV_dist_1.0_Protein_chain_E.itp

On Fri, Mar 1, 2019 at 10:53 AM morpheus <morpheus.sommer2008 at gmail.com>
wrote:

> Dear Gromacs users,
>
> I would like to run protein/protein interaction simulation (consisting of 5
> chains) that holds the backbone atoms rigid but allows side-chain
> movements. According to the Gromacs documentation this should work by:
>
> "Special position restraint .itp files can be created using the genrestr
> utility [...].  For example, if you wish to apply position restraints to
> only the backbone atoms of your protein, use genrestr and choose "Backbone"
> as the output group, and #include "backbone_posre.itp" in your topology."
> [1]
>
> I can generate the .itp file as described above but if I include it in my
> .top file then I get the following error:
>
> ###########
> Fatal error:
> [ file backbone_posre.itp, line 687 ]:
> Atom index (2472) in position_restraints out of bounds (1-2471).
> 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
> ###########
>
>
> My top file looks like below and I have added the #include
> "backbone_posre.itp" part manually.
>
>
> ###########
> ; Include forcefield parameters
> #include "gromos53a6.ff/forcefield.itp"
>
> ; Include chain topologies
> #include "2bnr_SLLDWITQV_dist_1.0_Protein_chain_A.itp"
> #include "2bnr_SLLDWITQV_dist_1.0_Protein_chain_B.itp"
> #include "2bnr_SLLDWITQV_dist_1.0_Protein_chain_C.itp"
> #include "2bnr_SLLDWITQV_dist_1.0_Protein_chain_D.itp"
> #include "2bnr_SLLDWITQV_dist_1.0_Protein_chain_E.itp"
> #include "backbone_posre.itp"
>
> ; Include water topology
> #include "gromos53a6.ff/spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
>
> ; Include topology for ions
> #include "gromos53a6.ff/ions.itp"
>
> [ system ]
> ; Name
> Protein in water
> ###########
>
> What does "different molecule" mean in the error message? It should apply
> to all protein chains ... or in other words: what do I need to change to
> make this one run?
>
> Thanks!!
>
> M
>
>
> [1] http://www.gromacs.org/Documentation/How-tos/Position_Restraints
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