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
