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://vt.edu/Pages/Personal/justin> >>> >>> <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> >>> >>> <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> >>> >>> <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-request@**gromacs.org<gmx-users-requ...@gromacs.org> >>> >. >>> Can't post? Read >>> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >>> >>> <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<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<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> >> > > -- > 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 thewww 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> > -- 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
