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

david.evans at ulsop.ac.uk david.evans at ulsop.ac.uk
Wed Jan 12 11:43:34 CET 2005


There is a method in the Amber package to run MD at constant pH,
where the protonation states of the amino acids are varied by an MC
method. I have never used it and don't work in this area myself, but
it's something to be aware of if you're starting a project. 


School of Pharmacy
University of London

---- Message from Xavier Periole <x.periole at rug.nl> at 2005-01-12
10:44:20 ------
>zjim wrote:
>> Hi
>> As both the basic and acidic amino acid will be different
>> state at different pH environment, the pH will greatly affect the
>> structure and function of protein. while the positions of hydrogen
>> 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
>> thank you in advice
>> zhou jinming
>Some remarks have been made about this subject during the few last
>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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