Re: [gmx-users] Best Force Field for a Membrane Protein
Hi Anirban, as far as I know the best force-field for membrane protein system is Charm36: it uses Charm27 for proteins but an improved parametrization for membrane lipids. I don't know if the lipids part has been already ported in gromacs format, but is a trivial task you can do in 1-2 days. Francesco Il giorno 19 aprile 2012 08:32, Anirban Ghosh reach.anirban.gh...@gmail.com ha scritto: Hi ALL, When running a membrane protein (say GPCR) in a lipid bilayer (say POPC or DPPC etc.) which according to your experience is the most suited force-field in GROMACS that best retains the 7TM / secondary structures of the protein over long simulations? I have tried running with ff53a6 (as suggested in Justin's tutorial), but find that the helices in the bilayer tend to lose their helicity over time and turns into coils. ff43a2 seems to do the job somewhat better by retaining the helicity. Will ff43a1 work even better as the principle aim is to observe changes in the protein without losing its secondary structures? Your experience please. Thanks a lot in advance. Regards, Anirban -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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] Best Force Field for a Membrane Protein
Hi, The CHARMM36 force field is already available, see the user contributions section on the GROMACS website. As for the original question on which is best, it is a hard question to answer. It really depends on what you need. For example, are you just looking at PC lipids in your membrane, or do you want to use lipids like PE, PG, etc. This may alter your choice of force field. Also be aware if you use an all-atom force field for your membrane (like CHARMM) your simulation will take substantially longer, but the protein model may be slightly better than one of the united-atom GROMOS force fields. You could also choose the combination of the united-atom Berger force field with an all-atom force field (OPLS or AMBER) for the protein. This seems like an attractive compromise but there has not been a huge amount of work looking at these combinations. You really will have to weigh up these different factors yourself and decide what is best for you. Also be aware that it is really important that once you have made the choice of force field, you use an appropriate set of simulation parameters for this force field. As for your point about the GROMOS 53A6 force field, it is know that this force field can have problems with short helices unwinding and there has been an update of this force field (GROMOS 54A7) to try and address these problems. We have been using this force field with no such issues. You can download the force field files from the ATB website (http://compbio.biosci.uq.edu.au/atb/). This might be the simplest solution for you, as you will not need to change your structure file (so no need to re-insert your protein into the membrane). Cheers Tom francesco oteri wrote: Hi Anirban, as far as I know the best force-field for membrane protein system is Charm36: it uses Charm27 for proteins but an improved parametrization for membrane lipids. I don't know if the lipids part has been already ported in gromacs format, but is a trivial task you can do in 1-2 days. Francesco Il giorno 19 aprile 2012 08:32, Anirban Ghosh reach.anirban.gh...@gmail.com mailto:reach.anirban.gh...@gmail.com ha scritto: Hi ALL, When running a membrane protein (say GPCR) in a lipid bilayer (say POPC or DPPC etc.) which according to your experience is the most suited force-field in GROMACS that best retains the 7TM / secondary structures of the protein over long simulations? I have tried running with ff53a6 (as suggested in Justin's tutorial), but find that the helices in the bilayer tend to lose their helicity over time and turns into coils. ff43a2 seems to do the job somewhat better by retaining the helicity. Will ff43a1 work even better as the principle aim is to observe changes in the protein without losing its secondary structures? Your experience please. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- Dr Thomas Piggot University of Southampton, UK. -- 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] Best Force Field for a Membrane Protein
Define long simulations? CHARMM27/36 in the sub-100ns timescale works for us. The following paper: Vanni, S., Neri, M., Tavernelli, I., and Rothlisberger, U.: Predicting Novel Binding Modes of Agonists to Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations. PLoS Comput Biol 7, e1001053 (2011) Uses Amber99SB over 500-800+ns for their beta2-adrenergic receptor system. On 2012-04-19 12:02:36PM +0530, Anirban Ghosh wrote: Hi ALL, When running a membrane protein (say GPCR) in a lipid bilayer (say POPC or DPPC etc.) which according to your experience is the most suited force-field in GROMACS that best retains the 7TM / secondary structures of the protein over long simulations? I have tried running with ff53a6 (as suggested in Justin's tutorial), but find that the helices in the bilayer tend to lose their helicity over time and turns into coils. ff43a2 seems to do the job somewhat better by retaining the helicity. Will ff43a1 work even better as the principle aim is to observe changes in the protein without losing its secondary structures? Your experience please. Thanks a lot in advance. Regards, Anirban -- 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] Best Force Field for a Membrane Protein
Hi ALL, Thanks a lot for the replies. By long simulation I mean 500 ns to 1000 ns. Has anybody tried with the ff43a1 with any membrane protein? Thanks, Anirban On Fri, Apr 20, 2012 at 3:26 AM, Peter C. Lai p...@uab.edu wrote: Define long simulations? CHARMM27/36 in the sub-100ns timescale works for us. The following paper: Vanni, S., Neri, M., Tavernelli, I., and Rothlisberger, U.: Predicting Novel Binding Modes of Agonists to Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations. PLoS Comput Biol 7, e1001053 (2011) Uses Amber99SB over 500-800+ns for their beta2-adrenergic receptor system. On 2012-04-19 12:02:36PM +0530, Anirban Ghosh wrote: Hi ALL, When running a membrane protein (say GPCR) in a lipid bilayer (say POPC or DPPC etc.) which according to your experience is the most suited force-field in GROMACS that best retains the 7TM / secondary structures of the protein over long simulations? I have tried running with ff53a6 (as suggested in Justin's tutorial), but find that the helices in the bilayer tend to lose their helicity over time and turns into coils. ff43a2 seems to do the job somewhat better by retaining the helicity. Will ff43a1 work even better as the principle aim is to observe changes in the protein without losing its secondary structures? Your experience please. Thanks a lot in advance. Regards, Anirban -- 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 -- 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
