On Sun, Jul 25, 2010, Xioling Chuang wrote:
>
> To calculate the energy components of complex, ligand and receptor using
> MM-PBSA (or MM-GBSA) by taking into account the salt effect (monovalent
> salt), in the "mm_pbsa.in" file how can we specify the type of ion, like
> NaCl, KCl, NaBr, etc.? What is the value of vdW radii of ions used in
> the calculation?
The mm-pbsa or mm-gbsa methods take account of salt by using Debye-Huckel
theory: only the ionic strength is relevant, not the chemical nature of the
salt, so there is no difference between NaCl and KCl, for example.
As I mentioned in a recent post, there is some recent (and not-so-recent)
interest in continuum solvent models that have explicit ions. This is an
interesting area of research, but such calculations are not currently
supported by Amber.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jul 25 2010 - 14:00:03 PDT
