Hi Jason,
Ok, thanks a lot!
Eric
On 3 March 2017 at 14:47, Jason Swails <jason.swails.gmail.com> 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
>
> --
> Jason M. Swails
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--
Eric Lang
BrisSynBio Postdoctoral Research Associate Modelling
Centre for Computational Chemistry
School of Chemistry - University of Bristol
Bristol BS8 1TS - United Kingdom
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Received on Fri Mar 03 2017 - 07:00:04 PST
