On Sat, May 18, 2013 at 10:20 AM, jnsong <jns...@itcs.ecnu.edu.cn> wrote:
> 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? > You need both molecules in the same [moleculetype], since the restraint directives require this. pdb2gmx -h will help here. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
