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

[Alessandra Villa]

Hi,

I guess the problem is that you do not have all the atoms (defined in the
restrains) one topology file. My suggestion is to use the  the option merge
to create one  topology file for protein and ligands and then add your
restraints definition there.
Best regards
Alessandra


On Thu, Dec 12, 2019 at 6:49 PM Sadaf Rani <sadafrani6 at gmail.com> wrote:

> 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
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