Hi,
On Wed, Aug 3, 2016 at 9:54 AM, Thomas Evangelidis <tevang3.gmail.com> wrote:
> The 'gbsa' parameter is set to 0 by default and when I set it to 1 or 2,
> the GB simulations as slowed down. Is the SASA calculation necessary,
> namely have the igb=1, 2, 5, 7 or 8 been optimized using gbsa=0 or not?
The polar (igb) and nonpolar (gbsa) solvation energy calculations are
separate, and to my knowledge no GB parameters have been optimized for
use with the nonpolar model in Amber. Whether the nonpolar
contribution is necessary depends on what kind of dynamics are going
on in your system. If the shape of your system will be relatively
static (i.e. the shape of your system isn't changing much due to
unfolding, large domain movements, etc) then it's probably safe to
assume that the nonpolar contribution would be relatively constant and
can probably be neglected. However, if your system is changing shape
dramatically one could expect a correspondingly large change in the
nonpolar solvation energy and you probably need to include it.
However, as Hai mentioned the nonpolar model that Amber has (which is
based on solvent-accessible surface area obtained from the very
approximate LCPO method) is not very accurate, and in my experience
pretty inaccurate when there are large changes in surface area. So if
you do decide to use it just be aware of these issues.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 03 2016 - 12:30:02 PDT
