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 >
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