Dear all,
Recently, I want to add angle_restraints and dihedral_restraints for
atoms in two separate molecules, that is, inter-molecular restraints,
not intra-molecular restraints.
I add the following into my .top file:
[ angle_restraints ]
; i j k l type theta0 fc multiplicity
20 22 47 50 1 0.0 1500 1
[ dihedral_restraints ]
; i j k l type label phi dphi kfac power
25 28 51 52 1 1 180 0 1 2
But it give errors:
"Fatal error:
[ file ang_res.itp, line 5 ]:
Atom index (47) in angle_restraints out of bounds (1-24).
This probably means that you have inserted topology section
"angle_restraints"
in a part belonging to a different molecule than you intended to."
Atom 20/22 belongs to one molecule, and Atom 47/50 belongs to another
molecule. The same situation is for atom 25/28 and atom 51/52.
I guess this error comes from the fact that I have two separate
molecules in my simulation system, thus topol_Protein.itp and
topol_Protein2.itp are produced when using pdb2gmx. Atom 47 in .gro file
has atom number 17 in topol_Protein2.itp. Thus it gives the error that
Atom index (47) in angle_restraints out of bounds!
Additionally, [ angle_restraints] and [dihedral_restraints] seems for
the intra-molecular interaction definitions.
Would you please tell me how to add angle and dihedral restraints for
the atoms that belong to two different molecules?
Thank you very much!
Best wishes!
Jianing Song
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