On Thu, Jul 21, 2011 at 7:37 PM, Rajesh Raju <rajesh.raju.mail.chem.tamu.edu
> wrote:
> Dear Amber users,
>
> I have question regarding the MMGB(PB)SA calculations:
>
> [1] How to chose the best value for saltcon variable in GB and istrng
> varibale in PB. i have seen in some tutorials its 0.1 or 0.15 etc....
>
Choose the value that's closest to the experimental value you're trying to
reproduce. Literature searches will help you here. Another thing to keep
in mind is that the "valid" range of saltcon for GB calculations is
significantly smaller than for PB (and the non-linear PB range is larger
than the linear PB range) due to the nature of the approximations used. GB
salt concentrations above 0.1 are generally discouraged, I think.
> [2] How much these variables can influence the total binding free
> eenrgy if we use some value other than the default value of 0.00
>
It will probably not have a huge effect generally -- it depends on how large
the polar solvation free energy is -- the larger the value, the more the
salt concentration can affect it. The only way to tell for sure is to use
both values on a small number of frames and compare the results.
> [3] How to chose the best values for surften/surfoff varibales in GB
> and cavity_surften/cavity_offset variables in PB..Can I use the
> default values?
>
I would suggest against adjusting these. They have been parametrized to
reproduce nonpolar solvation free energies in water, so you should keep the
default values. I would only suggest changing these if you want to
calculate the surface area instead of the nonpolar solvation energy (change
surften to 1, but keep offset the same), or you want to change solvents
(which is inadvisable for GB, anyway).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 22 2011 - 07:30:03 PDT
