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Hello,<br>
<br>
<div align="justify">Unfortunately there's no simple solution to this.
An initial model can be built by setting the protonation states
according to the pH - you can do it using pdb2gmx (in Gromacs). Then,
you need to refine your model by energy minimization. If you want to
run an MD simulation, that might be enough. However, if the pH that you
need to work with is much smaller or larger than the pH in which the
protein was crystallised, the protein may be deformed, and you may need
to equilibrate it for a long time before you get any meaningful model.<br>
</div>
<br>
Ran.<br>
<br>
zjim wrote:<br>
<blockquote type="cite" cite="mid41E4C096.00007D.12461@m185.163.com">Hi<br>
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? <br>
Maybe a soft will do, does somebody know it, please give some advice,.<br>
<br>
thank you in advice<br>
<br>
zhou jinming<br>
<br>
<br>
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Shanghai Institute of Organic Chemistry<br>
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<pre class="moz-signature" cols="72">--
------------------------------------------------------
Ran Friedman
Laser Laboratory for Fast Reactions in Biology
Department of Biochemistry
Faculty of Life Sciences
Tel-Aviv University
Tel. +972-3-6409824
Fax. +972-3-6409875
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