On Wed, Jun 20, 2012 at 9:00 AM, Nicholus Bhattacharjee <
nicholusbhattacharjee.gmail.com> wrote:
> Dear community,
>
> I am performing a constant pH simulation at pH 7. I have only included HIP
> as titratable residue. Is it alright or I need to include other titratable
> residues also. Thank you in advance.
>
There is no way to tell a priori, but most of the other titratable residues
(except for CYS, if you have a free cysteine residue) have reference pKas
far away from 7, so there's a good chance that it's OK.
My suggestion is to take a look at some of the experimental pKas -- if they
are within 1 to 1.5 pH units away from 7, I would strongly suggest
including them. If they are 2.5-3+ units from 7, it's probably safe to
omit them.
You could also run a short simulation titrating other residues just to try
it and see if it changes protonation state a lot.
HTH,
Jason
>
> Nicholus
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jun 20 2012 - 07:00:02 PDT
