Check Phys Rev Let 96 (2006) art nr 238102. You need simulations with reproducible folding so small peptides only.
Tot Ziens! Op 4 jan 2012 om 02:35 heeft bharat gupta <bharat.85.m...@gmail.com> het volgende geschreven: > Thanks for all your replies. I want to know this can be done in gromacs or > not - using REMD with structure based models generated from SMOG server to > study protein folding and unfolding ??. Also, I have a question about how to > determine the exchange probablities for a particular REMD experiment and > also how many replicas do we need to consider, does that depend on the > temperature list generated from the T_REMD server?? > > On Sat, Dec 31, 2011 at 11:36 AM, felmer...@uchile.cl <felmer...@uchile.cl> > wrote: > Yeah sure. There are several methods to trick your peptide to fold, but often > you loose the real kinetics by using them. I think a 230 residues protein is > too big to study folding kinetics through MD (because of the folding > kinetics, not the size of the system). With topology based potenitials > (Go-like models) you surely can do it, but take into account the the core > asumption there is that the energy landscape of your peptide is perfectly > funneled to the native state, which is a very good approximation for small > protein (like a 100 residues) but not so nice for bigger proteins. In fact, > even small proteins have intermediate states which makes the energy landscape > somehow rugged (the engrailed homeodomain, the trp repressor, etc). Besides > that, it is not a trivial task to go from the reduced representation to real > kinetic constants. Maybe if you are interested in comparison rather than > absolute values you can be lucky with the Go-modeling. If that is the case > maybe you should try the SMOG potential.... it is very fast. > > > > regards > > ----Mensaje original---- > De: bharat.85.m...@gmail.com > Fecha: 30-dic-2011 22:45 > > Para: "Discussion list for GROMACS users"<gmx-users@gromacs.org> > Asunto: Re: [gmx-users] Re: Folding rate > > The protein that I am dealing with is a 230 amino acid protein. I have come > across some methods that used reduced space model of protein such as CABS for > locating the protein folding pathway. An another paper describes about using > Go model together with Rigid body dynamics for finding protein folding > pathway. > > On Sat, Dec 31, 2011 at 10:23 AM, felmer...@uchile.cl <felmer...@uchile.cl> > wrote: > I small thing to consider with that particular paper is that DE Shaw has a > special machine (Anton) to do those calculations, so in principle it is not > possible to reproduce them (in a reasonable amount of time) on a regular > (super)computer. I think your best shot, if your protein is small enough, is > to use accelerated MD mixed with some good old kramer's theory. See for > example J. Chem. Theory Comput., 2011, 7 (3), pp 575–581. > > In any case it seems to me like too much of an effort, in the end here you > really rely in the accuracy of the forcefield. > > Regards > > > ----Mensaje original---- > De: jmda...@itqb.unl.pt > Fecha: 30-dic-2011 21:40 > Para: "Discussion list for GROMACS users"<gmx-users@gromacs.org> > Asunto: Re: [gmx-users] Re: Folding rate > > > As it was pointed out, the literature is vast on this subject. > > Moreover, calculating folding rates from simulations is not a trivial > subject, and it relies on many assumptions (e.g. what is considered "folded", > that the sampling obtained is enough). Even for small peptides, "enough > sampling" may mean several hundreds of microsseconds, something not > accessible to everyone. > > For a very recent article on the subject, check out: > > Lindorff-Larsen, K., Piana, S., Dror, R.O., Shaw, D.E. (2011) How > Fast-Folding Proteins Fold, Science 334:517-520. > http://dx.doi.org/10.1126/science.1208351 > > Regards, > João > > On Sat, Dec 31, 2011 at 12:19 AM, KS Rotondi <k...@chemistry.umass.edu> wrote: > As Justin pointed out, there is a vast literature on this topic, you need to > ask yourself what you seek, and look at many review articles to find some > reasonable starting points for you own needs and designs. Beyond that, it's a > lot of hard work... > > On Dec 30, 2011, at 7:04 PM, bharat gupta wrote: > > Thanks for your advice... Could you please refer me some papers regarding > this .... > > On Sat, Dec 31, 2011 at 8:17 AM, KS Rotondi <k...@chemistry.umass.edu> wrote: > No, there is no way to use such data to determine the folding rate of the > intact protein. If you used a fragment approach you could potentially (read > lots of papers on REMD) isolate nucleation sites, but minus the tertiary > interaction scheme you could not tell a compelling story. Now, if you want to > find nucleation sites and see if there are spatially proximal sites and > simulate them together... You might begin to tell a story. > > Ken > > > On Dec 30, 2011, at 6:09 PM, Justin A. Lemkul wrote: > > > > bharat gupta wrote: > Thanks for your reply. I want to whether does it make any sense or is it > possible to simulate fragments of proteins and find their folding rate and > then correlate it to folding rate of whole protein ?? > > Simulating arbitrary parts of a protein may or may not produce any relevant > information, likely the latter. Independently folding domains might be > simulated in isolation, but if there is a chance that the peptide sequences > have any effect on neighboring residues or even more distal sites, you'll > never produce anything useful. > > -Justin > > On Sat, Dec 31, 2011 at 8:00 AM, Justin A. Lemkul <jalem...@vt.edu > <mailto:jalem...@vt.edu>> wrote: > bharat gupta wrote: > Hi, > I want to know whether it's possible to calculate the folding > rate of 20 residue peptide folding into a beta-hairpin using > gromacs ?? > Anything is possible ;) But seriously, there is existing literature > on such topics, I suspect you can find methodology that will suit > your needs. > -Justin > -- ==============================__========== > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 > http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin > <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > ==============================__========== > -- gmx-users mailing list gmx-users@gromacs.org > <mailto: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 > <mailto:gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists > <http://www.gromacs.org/Support/Mailing_Lists> > -- > Bharat > Ph.D. Candidate > Room No. : 7202A, 2nd Floor > Biomolecular Engineering Laboratory > Division of Chemical Engineering and Polymer Science > Pusan National University > Busan -609735 > South Korea > Lab phone no. - +82-51-510-3680, +82-51-583-8343 > Mobile no. - 010-5818-3680 > E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 thewww interface or > send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > Bharat > Ph.D. Candidate > Room No. : 7202A, 2nd Floor > Biomolecular Engineering Laboratory > Division of Chemical Engineering and Polymer Science > Pusan National University > Busan -609735 > South Korea > Lab phone no. - +82-51-510-3680, +82-51-583-8343 > Mobile no. - 010-5818-3680 > E-mail : monu46...@yahoo.com > > -- > 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? 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Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > Bharat > Ph.D. Candidate > Room No. : 7202A, 2nd Floor > Biomolecular Engineering Laboratory > Division of Chemical Engineering and Polymer Science > Pusan National University > Busan -609735 > South Korea > Lab phone no. - +82-51-510-3680, +82-51-583-8343 > Mobile no. - 010-5818-3680 > E-mail : monu46...@yahoo.com > > > > > > -- > 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 > > > > -- > Bharat > Ph.D. Candidate > Room No. : 7202A, 2nd Floor > Biomolecular Engineering Laboratory > Division of Chemical Engineering and Polymer Science > Pusan National University > Busan -609735 > South Korea > Lab phone no. - +82-51-510-3680, +82-51-583-8343 > Mobile no. - 010-5818-3680 > E-mail : monu46...@yahoo.com > > -- > 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
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