Thank you very much
Rahul Ramesh
Masters Student
Department of Chemical Engineering
University of Michigan Ann Arbor
(+1 734-680-4453)
On Fri, Sep 18, 2015 at 5:04 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Fri, Sep 18, 2015 at 4:59 PM, Rahul Ramesh <raramesh.umich.edu> wrote:
>
> > Hey Jason
> > I am trying to calculate the reference energy for a hexane ring with a
> > -COOH side group. I get a value of ~-13 kcal/mol. I used the same partial
> > charge set for both the Thermodynamic Integration (TI) and CpHMD. I also
> > adjusted the value of partial charge on the beta carbon. I do not get a
> > change in protonation state. Previously, I tried Succinic Acid
> > (COOHCH2CH2COOH) and was able to use the reference energy from TI and got
> > 50% protonation at pH = pKa.
> > Does the size of the model compound affect the protonation state change?
>
>
> No. Size does not matter. It increases the likelihood that you will make
> a mistake when defining the charge vector in the titratable_residues.py
> file, but as long as you've done that right it should work fine.
>
>
>
> > If
> > the model compound is too big (say about 42 atoms), won't it not be able
> to
> > protonate/deprotonate?
>
>
> No.
>
>
>
> > I am using a hexane ring with a -COOH group as this
> > in future is going to be a part of a polymeric chain. As a result, this
> is
> > the smallest model compound I can think of.
> > The EGB values in my simulation are pretty off compared to my del G value
> >
>
> The EGB values of a single protonation state are unrelated to the
> reference energy. Now, if you do a GB calculation in both protonation
> states and then *subtract* the sum of the EELEC/EGB energies, then that
> should be reasonably close to the computed reference energy. If it's not,
> there is a mistake somewhere.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Fri Sep 18 2015 - 14:30:05 PDT
