Re: [gmx-users] NBFIX to gromacs
Dear Mr. Lai, I see. I'll look more deeply into it, thanks for your answer. Ricardo. De: Peter C. Lai p...@uab.edu Para: Ricardo O. S. Soares ross_...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org Enviadas: Quarta-feira, 2 de Maio de 2012 20:35 Assunto: Re: [gmx-users] NBFIX to gromacs 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 listgmx-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
Re: [gmx-users] NBFIX to gromacs
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 listgmx-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
Re: [gmx-users] NBFIX to gromacs
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 listgmx-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 listgmx-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
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 listgmx-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 listgmx-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
