Hi
It is not clear to me what you want to do.
Why would the two histidines have a different reference free energy? If
the reference compound is the free histidine in solution, then it has
just the two regular pkas. CphMD would then compute the delta pka from
that value, when they are inside the protein.
The fact that the two histidines have different pkas inside the protein
should be a result of the cphmd calculation, not the input to it.
adrian
On 3/3/17 9:47 AM, Jason Swails wrote:
> 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
>
--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Fri Mar 03 2017 - 07:00:03 PST
