On Fri, Mar 3, 2017 at 9:33 AM, Eric Lang <eric.lang.bristol.ac.uk> wrote:
> Hello,
>
> I was wondering, if I want to correct the reference energy for Histidine
> residue can I use the same formula TI = Ref Energy + R*T*ln(10)*pKa ? In
> that case how do I deal with the two sites that have a different pKa?
> Can I just run the pH-REMD (at pH = pKa ± 0.1 pKa ± 0.2 pKa ± 1.2) using
> pKa=6.5 and then do the same for pKa=7.1 and then correct TI for each pKa?
> It sounds too simple to do that in the case of His and I fell like there is
> more hidden complexity because of the two sites?
>
​What I did was hack the cpinutil.py script to turn turn off one state (so
the generated cpin file only contained one protonation state). Treat this
the same way you would any non-tautomeric state.​
Do the same thing for the other site, and you have your two reference
energies.
HTH,
Jason
--
Jason M. Swails
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Received on Fri Mar 03 2017 - 07:00:02 PST
