[gmx-users] how to add angle_restraints and dihedral_restraints for atoms belonging to two different molecules
jnsong at itcs.ecnu.edu.cn
Sat May 18 10:20:52 CEST 2013
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:
[ 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
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!
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