[gmx-users] How to built a protein model basing on the X-ray diffraction structure at different pH environment

Xavier Periole x.periole at rug.nl
Wed Jan 12 10:44:20 CET 2005

zjim wrote:

> Hi
> As both the basic and acidic amino acid will be different protonation
> state at different pH environment, the pH will greatly affect the
> structure and function of protein. while the positions of hydrogen is
> hard to be earned using X-ray diffraction method, Is there a way to
> built protein models at different pH environment basing on a X-ray
> diffraction structure?
> Maybe a soft will do, does somebody know it, please give some advice,.
> thank you in advice
> zhou jinming

Some remarks have been made about this subject during the few last months.
You should be able to find them by searching the user-list archive.
You basicaly have to define the protnation state of the titratable
groups in your
protein using a method of your choice.



   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at rug.nl
   web-page: http://md.chem.rug.nl/~periole

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