"It doesn't work" is not enough information to lead anyone to a solution :-)
Mark On Thu, Aug 22, 2013 at 6:53 PM, Shima Arasteh <shima_arasteh2...@yahoo.com> wrote: > If you mean that I need to modify the posre_ion.itp file to: > > ; position restraints for a_85563 of system > > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 100000 100000 100000 > > It doesnt work.......... :-( > > > Sincerely, > Shima > > > ----- Original Message ----- > From: Mark Abraham <mark.j.abra...@gmail.com> > To: Shima Arasteh <shima_arasteh2...@yahoo.com> > Cc: Discussion list for GROMACS users <gmx-users@gromacs.org> > Sent: Thursday, August 22, 2013 6:37 PM > Subject: Re: [gmx-users] position restraint > > Now you have a [moleculetype] with one atom and hopefully a position > restraint. But its [position_restraints] wants to act on atom 85563 of > the molecule, which does not exist! See newly updated > http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds > > Mark > > On Thu, Aug 22, 2013 at 3:58 PM, Shima Arasteh > <shima_arasteh2...@yahoo.com> wrote: >> So I made a specific ces.itp file, and made a separate section in top file : >> ces.itp file: >> [ moleculetype ] >> ; molname nrexcl >> Ces 1 >> >> [ atoms ] >> ; id at type res nr residu name at name cg nr charge >> 1 CES 1 Ces Ces 1 1 >> >> >> .top file: >> ; Include topology for ces >> #include "ces.itp" >> #ifdef POSRES_ION >> #include "posre_ion.itp" >> #endif >> ; Include topology for ions >> #include "./charmm36-modified.ff/ions.itp" >> >> >> The posre_ion.itp file contains: >> >> ; position restraints for a_85563 of system >> >> [ position_restraints ] >> ; i funct fcx fcy fcz >> 85563 1 100000 100000 100000 >> >> But it doesnt work, would you please let me know if I had a mistake? >> >> Thanks for your suggestions in earlier messages. >> >> >> >> Sincerely, >> Shima >> >> >> ----- Original Message ----- >> From: Mark Abraham <mark.j.abra...@gmail.com> >> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS >> users <gmx-users@gromacs.org> >> Cc: >> Sent: Thursday, August 22, 2013 5:54 PM >> Subject: Re: [gmx-users] position restraint >> >> Have a look at that file. It defines the [moleculetype] for lots of >> ions, but you need a position restraint that applies to whichever >> [moleculetype] is the one you want to use. That means it has to come >> before the next [moleculetype]. As manual 5.7 says, the .top format is >> hierarchical. So you need to modify the ions.itp, or make one that has >> only the ion of interest. >> >> Mark >> >> On Thu, Aug 22, 2013 at 3:01 PM, Shima Arasteh >> <shima_arasteh2...@yahoo.com> wrote: >>> Yes, >>> But the part in which the ions are introduced is #include >>> "./charmm36-modified.ff/ions.itp" , >>> Is this not the right place to write the posre_ion lines? As I see it is in >>> agreement with "Atom index n in position_restraints out of bounds" link. >>> So what would be the solution? I don't see any itp file generated by >>> pdb2gmx, for the ions such as chain A and other moleculetypes ? >>> >>> Would you give me a hint and help me with it please? >>> >>> Sincerely, >>> Shima >>> >>> >>> >>> ---------- Forwarded message ---------- >>> From: Shima Arasteh <shima_arasteh2...@yahoo.com> >>> Date: Thu, 22 Aug 2013 03:54:07 -0700 (PDT) >>> Subject: [gmx-users] position restraint >>> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >>> >>> Hi, >>> >>> I want to put position restraint on an ion , >>> >>> First made an .itp file of the ion: posre_ion.itp >>> >>> Then added these line to top file: >>> #include "./charmm36-modified.ff/ions.itp" >>> #ifdef POSRES_ION >>> #include "ion_posre.itp" >>> #endif >>> >>> And added the line to mdp file >>> >>> define = -DPOSRES_ION >>> >>> But the grompp failed because it gives me the fatal error that the >>> include line is not in the correct position. >>> >>> >>> >>> Would you please let me know if the inclusion of posre_ion.itp is not >>> as I did? What's the problem? >>> >>> Thanks in advance for your suggesions. >>> >>> Sincerely, >>> Shima >>> -- >>> 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 >>> >>> -- >>> 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 >> > -- 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
