On Tue, May 21, 2013 at 11:31 AM, jnsong <jns...@itcs.ecnu.edu.cn> wrote:
> Dear Mark, > > Thank you very much for your help! > > I add the restraints into my topol.top successfully! > > But there is still two questions: > > (1) After [angle_restraints] is added into my .top file, should I write > additional parameters into .mdp file to run > angle restraints? Because after [diheral_restrints] is added to .top file, > extra parameters of dihedral constraint should be added to .mdp file to > function. > Table 5.5 and manual 7.3 know more than I do about this ;-) > (2) Could [position_restraint] and [angle_restraint] be used together in > the same .mdp file? For example, I add position restraints to all the heavy > atoms of my protein, then I add [angle_restraint] to atom 20/22;47/58, is > this > reasonable? > There's no prohibition. Whether such a combination is reasonable depends, and is up to you to judge. Mark > > Thank you very much! > > Best wishes! > > Jianing > > > > > On 2013-05-18 16:43, Mark Abraham wrote: > >> 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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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
