[gmx-users] setting distance restraints between atoms belonging to different residues

[Sadaf Rani]

Hi gromacs users
I want to restraint distance, angles and dihedrals between atoms of two
different residues; In my case protein atom and ligand atom. Could anybody
suggest me the right way of doing it?
I have set topology file of complex as below:-

 Include forcefield parameters
#include "amber99sb-ildn.ff/forcefield.itp"

#include "atomtypes.itp"
#include "Protein.itp"
#include "lig1.itp"

 distance restraints
[ bonds ]
;    i     j  type     r0A     r1A     r2A    fcA    r0B     r1B     r2B
 fcB
  3437  3439    10     0.408   0.408   10.0   0.0    0.408   0.408   10.0
4184.000

[ angle_restraints ]
;   ai    aj    ak    al  type    thA      fcA    multA  thB      fcB
 multB
  3439  3437  3437  7908     1    162.37   0.0    1     162.37    162.37
 1
  3437  7908  7908  7906     1    112.53   0.0    1     112.53    112.53
 1

[ dihedral_restraints ]
;   ai    aj    ak    al   type    phiA     dphiA  fcA    phiB      dphiB
 fcB
  3439  3437  7908  7906     1    118.72   0.0    0.0    118.72    0.0
 41.840
  3437  7908  7906  7907     1    -69.05   0.0    0.0    -69.05    0.0
 41.840
  3430  3439  3437  7908     1    178.56   0.0    0.0    178.56    0.0
 41.840
#include "lig2.itp"
#include "lig3.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre_complex.itp"
#endif

; Include water topology
#include "amber99sb-ildn.ff/tip3p.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 "amber99sb-ildn.ff/ions.itp"
but it gives me the following error:-

ERROR 1 [file complex.top, line 9]:
  Atom index (7908) in bonds out of bounds (1-7893).
  This probably means that you have inserted topology section "bonds"
  in a part belonging to a different molecule than you intended to.
  In that case, move the "bonds" section to the right molecule.

How should I fix my topology file that I may not give this error?

Many thanks in advance

Sadaf