Thanks Erik for the information. On Tue, Mar 29, 2011 at 9:11 PM, Erik Marklund <er...@xray.bmc.uu.se> wrote:
> Having only browesd through the papaer very briefly, I can't see how the > protonation state was chosen. The modelling part of the paper wasn't that > informative. There is a web service called H++ that can make pKa estimates > for titrating sites. Not sure how accurate it is though. It uses continuum > electrostatics that may not be accurate enough for pKa estimates (see e.g. > reviews by Warshel from 1991 and 2006). I've never used H++ myself, only > heard about it. > > Erik > > Monisha Hajra skrev 2011-03-29 17.31: > > Thanks Justin. I haven't find any such tutorial or exact relevant research > paper. Find some paper though ( > http://peds.oxfordjournals.org/content/16/12/1017.full.pdf+html ), not > sure how they have done. > > On Tue, Mar 29, 2011 at 8:51 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > >> >> >> Monisha Hajra wrote: >> >>> Friends, >>> >>> Need a Gromacs tutorial to find effect of pH on catalytic side. Any help? >>> >> >> There probably isn't one. If it isn't at >> http://www.gromacs.org/Documentation/Tutorials or you can't find it with >> Google, then it doesn't exist. >> >> You'll probably want to look into the ability of pdb2gmx to alter side >> chain protonation state, and otherwise base your procedures on published >> literature. You may need to use QM/MM rather than vanilla MD for this type >> of process, depending on your system and your goals. >> >> -Justin >> >> >>> Regards >>> >>> >>> >> -- >> ======================================== >> >> 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 >> > > > > -- > ----------------------------------------------- > Erik Marklund, PhD student > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 755er...@xray.bmc.uu.se > http://folding.bmc.uu.se/ > > > -- > 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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