Aw: [gmx-users] Force Field for peptides and proteins
There isnt one it depends on your experiment, and what factors you take into account such as resources, time available or what you wish to observe. All atom is more realistic, but if time retraints or computer resources are limiting, you may wish a partial atom or hybrid atom system. In addition, difference in simply looking at domain changes in proteins or affinites, etc... Gesendet:Montag, 12. August 2013 um 14:19 Uhr Von:Maria Astn Serrano m.aston.serr...@gmail.com An:gmx-users@gromacs.org Betreff:[gmx-users] Force Field for peptides and proteins Dear Gromacs users, We would like to know which is the Force Field which is customarily preferred for simulations of peptides and proteins. Thank you very much. Best regards, Maria -- 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 dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant 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] Force Field for peptides and proteins
Dear Gromacs users, We would like to know which is the Force Field which is customarily preferred for simulations of peptides and proteins. Thank you very much. Best regards, Maria -- 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] Force Field for peptides and proteins
It depends on what properties of peptides and proteins that you want to explore. ~Thu On Mon, Aug 12, 2013 at 7:19 PM, Maria Astón Serrano m.aston.serr...@gmail.com wrote: Dear Gromacs users, We would like to know which is the Force Field which is customarily preferred for simulations of peptides and proteins. Thank you very much. Best regards, Maria -- 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] Force Field for peptides and proteins
I like CHARMM. Dr. Vitaly V. Chaban On Mon, Aug 12, 2013 at 2:19 PM, Maria Astón Serrano m.aston.serr...@gmail.com wrote: Dear Gromacs users, We would like to know which is the Force Field which is customarily preferred for simulations of peptides and proteins. Thank you very much. Best regards, Maria -- 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] Force Field for peptides and proteins
On 8/12/13 8:19 AM, Maria Astón Serrano wrote: Dear Gromacs users, We would like to know which is the Force Field which is customarily preferred for simulations of peptides and proteins. Interestingly, this same question was just asked on the development list, although the discussion indeed belongs here. http://lists.gromacs.org/pipermail/gmx-developers/2013-August/007016.html There is a wide body of literature on this topic, and it is very educational to read through as much of it as you can. Some force fields, like AMBER94 and CHARMM22+CMAP are decidedly too helical, while others (Gromos96 53A6 being a good example) tend to understate helices and overstate extended configurations. New parameter sets like AMBER99SB-ILDN and CHARMM22* are often used in protein folding studies and seem to do quite well. I think, in the end, it depends to some extent about the scope of what you are doing and the protein(s) to be studied. Even high quality force fields that perform well for folded proteins do not necessarily perform well on intrinsically disordered proteins or model peptides. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Force Field for peptides and proteins
On this note, I wanted to ask about simulated unfolding of proteins. I have a primarily alpha-helical-protein ( about 300 amino acids, 5 alpha helices, no beta strands) and 3 of its single point mutants. Now, to answer the question of relative stability, I want to place them in a water bath and heat them until they unfold. The temperature at which they unfold should qualitatively tell me which is more stable (the most stable unfolding at the highest temperature). I have been wondering which forcefield would be more suitable. I intend to use simulated heating at a constant rate (simulated annealing option in .mdp file). Any answers will be greatly appreciated. Thank you. On Mon, Aug 12, 2013 at 6:29 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/12/13 8:19 AM, Maria Astón Serrano wrote: Dear Gromacs users, We would like to know which is the Force Field which is customarily preferred for simulations of peptides and proteins. Interestingly, this same question was just asked on the development list, although the discussion indeed belongs here. http://lists.gromacs.org/**pipermail/gmx-developers/2013-** August/007016.htmlhttp://lists.gromacs.org/pipermail/gmx-developers/2013-August/007016.html There is a wide body of literature on this topic, and it is very educational to read through as much of it as you can. Some force fields, like AMBER94 and CHARMM22+CMAP are decidedly too helical, while others (Gromos96 53A6 being a good example) tend to understate helices and overstate extended configurations. New parameter sets like AMBER99SB-ILDN and CHARMM22* are often used in protein folding studies and seem to do quite well. I think, in the end, it depends to some extent about the scope of what you are doing and the protein(s) to be studied. Even high quality force fields that perform well for folded proteins do not necessarily perform well on intrinsically disordered proteins or model peptides. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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
