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.html<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 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) 706-7441 > > ==============================**==================== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://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 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
