[gmx-users] Effect of pH on catalytic side

[Erik Marklund]

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 <jalemkul at vt.edu 
> <mailto:jalemkul at 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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>     -- 
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at 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-request at gromacs.org
>     <mailto:gmx-users-request at 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 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110329/79cbf1a8/attachment.html>