On Wed, May 2, 2012 at 7:21 PM, Jesper Soerensen <jesorensen.ucsd.edu>wrote:
> Hi Jason,
>
> I know and that does make sense, since the changes only pertain to the
> protein. But then mbondi2 were not made for ligands either - correct?
> So should the ligand radii not come from the gaff parameters, or am I
> misunderstanding something and gaff does not contain/specify its own set of
> GB radii but instead use the mbondi2 radii?
>
As far as I know, they were not developed with small ligands in mind.
However, my understanding is that GB does reasonably well for small
ligands, since it's not a significant perturbation from the Born solution
to the PB equation (from which GB is based). The complexity arises when
you try to treat very complex systems like proteins.
Globular proteins are obviously significantly different than a simple
sphere, and so the correct estimation of the effective Born radius (which
more or less measures proximity to the bulk solvent) becomes essential to
properly characterize the solution-phase behavior. This is what the
intrinsic radii from %FLAG RADII are used for (and *only* this in GB
calculations). As a result, you should consider these radii a parameter of
the GB model you're using, not of the force field you're using. (So no,
gaff does not contain its own set of GB radii, nor does any other Amber
force field).
A gaff carbon that is sp2-bonded carbon with a double-bond to an oxygen is
for all intents and purposes identical to the backbone C atom of an amino
acid with respect to relative size and is therefore treated the same with
the LEaP-assigned radii. Moreover, I argue this is the appropriate
behavior given the purpose these radii serve.
> Also, is mbondi2 the standard PB radii in leap now?
>
No, 'mbondi' is (at least using ff12SB).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed May 02 2012 - 17:30:03 PDT
