Re: [AMBER] Addition of hydrogens - isoelectric point of protein

From: Adrian Roitberg <roitberg.ufl.edu>
Date: Thu, 25 Mar 2021 15:14:21 -0400

Neither.

You need to setup the pH at whatever the experiment was done.

If you are simulating a system that was or will be studied at pH 5, you
need to use that.

Adrian


On 3/25/21 3:11 PM, Prasanth G, Research Scholar wrote:
> [External Email]
>
> Dear all,
> During the protein preparation using a webserver like H++, is it better to
> specify the pH equal to (or around) the isoelectric point of the protein or
> do we have to specify the pH of the protein's environment (usually pH of
> 7.4)?
> I would be grateful if you could help me in getting a clarity about the
> same.
> Thank you in advance.
> --
> Regards,
> Prasanth.
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-- 
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Thu Mar 25 2021 - 12:30:03 PDT
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