On Tue, Jul 21, 2015 at 11:22 AM, Arjun Sharma <arjunsharma83.gmail.com>
wrote:
> Dear Jason,
>
> Under the Testing the titratable group definitions section (AMBER 14
> manual, page 402)
> # Cysteine
> refene1 = _ReferenceEnergy(igb2=77.4666763, igb5=76.2588331,
> igb8=71.5804519)
> refene1.solvent_energies(igb2=77.6041407, igb5=76.2827217)
> What exactly is difference between two values of igb2 in refene1 and
> refene1.solvent_energies lines above ? I understand that the reference
> energy calculated from TI is used here, but I don’t understand, why are
> there two reference energy values with a small difference ?
>
solvent_energies are the reference energies for the reference compound
using that GB model, but with the dynamics run in explicit solvent. (This
is what is called explicit solvent CpHMD in Amber parlance.)
The reference energies *should* be roughly equivalent, but conformational
differences between the implicit and explicit dynamics are enough to
require slight changes to the reference energy for the titration to yield
the correct pKa for the model compound in explicit solvent.
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 Tue Jul 21 2015 - 09:30:02 PDT
