Re: how to set pH

From: Jérôme Hénin (
Date: Wed Mar 31 2010 - 06:29:20 CDT


To describe pH in your system, you should look at titratable residues
in the protein, and decide in which protonation states these are most
likely to be. There are various tools to do this, depending on how
critical it is for you to get this right. I recommend doing some
bibliographic research on pKa prediction for titratable residues in
proteins, prediction of protonation states, etc.


2010/3/31 crazylyf <>:
> Hi ,
> I am a freshman in this field and I have a question recently. I want to run
> a simulation that has a certain pH outside of a membrane protein. Is there
> any way can I achieve this?
> Thank you very much.
> Regards,
> Crick

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