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

[morpheus]

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