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
