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, [email protected] <[email protected]>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: [email protected] > Fecha: 30-dic-2011 22:45 > > Para: "Discussion list for GROMACS users"<[email protected]> > 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, [email protected] <[email protected] > > 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: [email protected] >> Fecha: 30-dic-2011 21:40 >> Para: "Discussion list for GROMACS users"<[email protected]> >> 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 <[email protected]>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 <[email protected]>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 <[email protected]<mailto: >>>>>> [email protected]>> 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 [email protected] >>>>>> <mailto:[email protected]> >>>>>> 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 [email protected] >>>>>> <mailto:[email protected]>. >>>>>> 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 : [email protected] <mailto:[email protected]> >>>>>> >>>>> >>>>> -- >>>>> ======================================== >>>>> >>>>> 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 [email protected] >>>>> 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 [email protected]. >>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>> >>>> -- >>>> gmx-users mailing list [email protected] >>>> 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 [email protected]. >>>> >>>> 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 : [email protected] >>> >>> -- >>> gmx-users mailing list [email protected] >>> 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 [email protected]. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> >>> -- >>> gmx-users mailing list [email protected] >>> 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 [email protected]. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> >> -- >> João M. Damas >> PhD Student >> Protein Modelling Group >> ITQB-UNL, Oeiras, Portugal >> Tel:+351-214469613 >> >> >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> 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 : [email protected] > > > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > 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 : [email protected]
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