Re: [gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF
On 27/04/2012 5:21 AM, Ricardo O. S. Soares wrote: Dear users, In GROMACS, does CHARMM36 ff, calculate eventual 1-4 interactions that are absent from the [pairtypes] section of the ffnonbonded.itp file? I ask this because I'm converting cholesterol parameters from CHARMM36c to gmx format, and several 1-4 values are absent in the last two columns of the prm file. Does setting gen_pairs to yes in the [defaults] section in the forcefield.itp work? Probably. What documentation exists is probably in the walk-through example of manual 5.7.1. You can probably construct yourself a trivial test case if you wish to verify how things work. Mark -- 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] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF
Hi Mark, yeah, I'll try it. Thanks for your reply, Ricardo. De: Mark Abraham mark.abra...@anu.edu.au Para: Discussion list for GROMACS users gmx-users@gromacs.org Enviadas: Sexta-feira, 27 de Abril de 2012 10:43 Assunto: Re: [gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF On 27/04/2012 5:21 AM, Ricardo O. S. Soares wrote: Dear users, In GROMACS, does CHARMM36 ff, calculate eventual 1-4 interactions that are absent from the [pairtypes] section of the ffnonbonded.itp file? I ask this because I'm converting cholesterol parameters from CHARMM36c to gmx format, and several 1-4 values are absent in the last two columns of the prm file. Does setting gen_pairs to yes in the [defaults] section in the forcefield.itp work? Probably. What documentation exists is probably in the walk-through example of manual 5.7.1. You can probably construct yourself a trivial test case if you wish to verify how things work. Mark -- 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] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF
btw you only need explicit 1-4 for charmm when the 1,4 from the original charmm prm is actually different/specified (i.e. non-conjugated carbons) -- Sent from my Android phone with K-9 Mail. Please excuse my brevity. Ricardo O. S. Soares ross_...@yahoo.com.br wrote: Hi Mark, yeah, I'll try it. Thanks for your reply, Ricardo. _ De: Mark Abraham mark.abra...@anu.edu.au Para: Discussion list for GROMACS users gmx-users@gromacs.org Enviadas: Sexta-feira, 27 de Abril de 2012 10:43 Assunto: Re: [gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF On 27/04/2012 5:21 AM, Ricardo O. S. Soares wrote: Dear users, In GROMACS, does CHARMM36 ff, calculate eventual 1-4 interactions that are absent from the [pairtypes] section of the ffnonbonded.itp file? I ask this because I'm converting cholesterol parameters from CHARMM36c to gmx format, and several 1-4 values are absent in the last two columns of the prm file. Does setting gen_pairs to yes in the [defaults] section in the forcefield.itp work? Probably. What documentation exists is probably in the walk-through example of manual 5.7.1. You can probably construct yourself a trivial test case if you wish to verify how things work. Mark -- 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 -- 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] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF
Oh, I see. I did inserted only the provided values from CHARMM ff prm file. Now I'll do some testing... Thanks Peter, --- Ricardo O. S. Soares , PhD Student. Group of Biological Physics - Department of Physics Chemistry Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo. Av.do Café, S/N - ZIP:14040-903 - Ribeirão Preto, São Paulo, Brazil. Phone: +55 16 36024840. Curriculum Lattes:http://lattes.cnpq.br/0777038258459931 ross_...@yahoo.com.br,rsoa...@fcfrp.usp.br De: Peter C. Lai p...@uab.edu Para: Discussion list for GROMACS users gmx-users@gromacs.org; gmx gromacs gmx-users@gromacs.org Enviadas: Sexta-feira, 27 de Abril de 2012 18:39 Assunto: Re: [gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF btw you only need explicit 1-4 for charmm when the 1,4 from the original charmm prm is actually different/specified (i.e. non-conjugated carbons) -- Sent from my Android phone with K-9 Mail. Please excuse my brevity. Ricardo O. S. Soares ross_...@yahoo.com.br wrote: Hi Mark, yeah, I'll try it. Thanks for your reply, Ricardo. De: Mark Abraham mark.abra...@anu.edu.au Para: Discussion list for GROMACS users gmx-users@gromacs.org Enviadas: Sexta-feira, 27 de Abril de 2012 10:43 Assunto: Re: [gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF On 27/04/2012 5:21 AM, Ricardo O. S. Soares wrote: Dear users, In GROMACS, does CHARMM36 ff, calculate eventual 1-4 interactions that are absent from the [pairtypes] section of the ffnonbonded.itp file? I ask this because I'm converting cholesterol parameters from CHARMM36c to gmx format, and several 1-4 values are absent in the last two columns of the prm file. Does setting gen_pairs to yes in the [defaults] section in the forcefield.itp work? Probably. What documentation exists is probably in the walk-through example of manual 5.7.1. You can probably construct yourself a trivial test case if you wish to verify how things work. Mark -- 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 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
[gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF
Dear users, In GROMACS, does CHARMM36 ff, calculate eventual 1-4 interactions that are absent from the [pairtypes] section of the ffnonbonded.itp file? I ask this because I'm converting cholesterol parameters from CHARMM36c to gmx format, and several 1-4 values are absent in the last two columns of the prm file. Does setting gen_pairs to yes in the [defaults] section in the forcefield.itp work? 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
