Re: [AMBER] Story of bugfix 18-Amber10

From: case <>
Date: Wed, 19 Jan 2011 22:43:52 -0500

On Wed, Jan 19, 2011, Eliac Brown wrote:

> I was wondering what is the story of bugfix 18 in amber10.
> I put an extra point on my ligand for better hydrogen bond description
> with the active site, and calculated the GBSA energy without any
> problem.
> So, why you implemented bugfix 18 which asks for no GB with extra-pint?

The amber GB force fields have never been parameterized with extra-point
protein or nucleic acid potentials. Under most circumstances, try to combine
those two would be a mistake. In particular, there are no default dielectric
radii to use for extra points.

If you understand the code well enough to add your own extra points, and to be
sure that you are not seeing any problem, then it is easy enough for you to
disable the check that bugfix 18 introduced.


AMBER mailing list
Received on Wed Jan 19 2011 - 20:00:03 PST
Custom Search