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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 18 2015 - 14:30:02 PDT
