The problem is that functype 1 for [ pairtypes ] when gromacs uses a CHARMM forcefield is that gromacs treats them as 1-4 interactions. You will have to ask/wait for someone familiar with the gromacs source to say if there is a different functype available to use to override non-1-4 interactions with the given pair parameters that you want to specify.
On 2012-05-02 12:35:17PM -0700, Ricardo O. S. Soares wrote: > Dear Mr. Peter C. Lai, > > I appreciate your kind response. > > I apologize for the delay on my part. > This NBFIX parameters that I'm working with came from the str file in > http://terpconnect.umd.edu/~jbklauda/research/download/chol_new.str , which > dates from 2012. > I successfully converted this whole file, now I'm wondering about this NBFIX > section. > I'm thinking about converting these values from Kcal to KJ and Angstrom to > nm, adapt and append to [ pairtypes ]. Could this be the right move? > Thanks again, > > Ricardo. > > > > > > > >________________________________ > > De: Peter C. Lai <p...@uab.edu> > >Para: Discussion list for GROMACS users <gmx-users@gromacs.org> > >Enviadas: Segunda-feira, 30 de Abril de 2012 20:46 > >Assunto: Re: [gmx-users] NBFIX to gromacs > > > >NBFIXes haven't been used in charmm for a long time (1998), although > >current versions still read topologies containing those records. Perhaps you > >should reparameterize your molecule with a more current version? (Or start > >with > >the coordinate file and use pdb2gmx with the converted ff). The only thing I > >can think of if you really need to do it is to create new atom types. > >As far as I know, gromacs only supports 1 set of vdw coefficients and a 1-4 > >pair. > > > > > > > >On 2012-04-30 01:30:59PM -0700, Ricardo O. S. Soares wrote: > >> Hello GMX users, > >> > >> does anyone that dealt with Charmm before knows how to translate the NBFIX > >> section into a Gromacs ff format? After convertion from KCal to KJ, does > >> it go into [pairtypes]? > >> I see that it concerns to corrections in LJ interactions, however the > >> charmm documentation seems a bit unclear to me. > >> > >> Thanks again, > >> Ricardo. > > > >> -- > >> 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 > > > > > >-- > >================================================================== > >Peter C. Lai | University of Alabama-Birmingham > >Programmer/Analyst | KAUL 752A > >Genetics, Div. of Research | 705 South 20th Street > >p...@uab.edu | Birmingham AL 35294-4461 > >(205) 690-0808 | > >================================================================== > > > >-- > >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 -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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