Hello,
The pKas of the 2 carboxylate residues are 4.0 for ASP and 4.4 for GLU.
Those for TYR and LYS are 9.6 and 10.4, respectively. Histidine has 2 pKas
for its 2 titratable sites, 6.5 and 7.1 for HID and HIE, respectively. At
pH 7 I would say you need to titrate Histidine residues. However, if any of
the other residues are solvent exposed (and you expect them to stay that way
during the entire simulation), you can probably safely omit those, too. The
only residues you have to include are those that you think may have their
pKas perturbed to the region of pKas that you're simulating at.
However, including more titratable residues does not increase the
computational cost of the simulation (it simply affects how often each
residue is titrated, on average). Since conformational sampling is the
bottleneck in CpH simulations and not protonation state sampling, typically,
this is not typically a big deal.
Hope this helps,
Jason
On Sat, Jul 31, 2010 at 10:19 AM, nicholus bhattacharjee <
nicholusbhattacharjee.gmail.com> wrote:
> Dear community,
> It is written in the amber manual that constant
> pH simulation donot support titrating the terminal residues. So we have to
> exclude them. Moreover we should exclude TYR and LYS for acidic simulations
> and GL4 and AS4 for basic simulations. My query is if I keep the
> solvph=7.00
> which residues should I exclude while simulating. Thank you in advance.
>
> --
> Nicholus Bhattacharjee
> PhD Scholar
> Department of Chemistry
> University of Delhi
> Delhi-110007 (INDIA)
> Phone: 9873098743(M)
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Jul 31 2010 - 08:00:03 PDT
