On Fri, Oct 15, 2010, Antonija Tomić wrote:
> When I choose to calculate both GB (GB=1) and PB (PB=1) in
> mm_pbsa_Binding.in script, MM energies, more precisely ELE term, seems
> not to depend on dielectric constant, i.e. I always get the same value
> for ELE. On the other hand, when I switch off GB calculations (using
> GB 0 in mm_pbsa_Binding.in script) values for ELE are scaled according
> to selected dielectric constant.
There is still an old option (dielc) that allows a uniform dielectric function
to be used in MM calculations that don't have any other solvent model. This
is not of much use for atomic-level models, but can be useful for
coarse-grained potentials, or for trying to reproduce literature results that
use this model, or for other specialized calculations.
When you use a solvent model like PB or GB, they have their own, non-uniform
dielectric models, which are controlled by intdiel and extdiel. The value of
dielc is ignored.
....dac
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Received on Fri Oct 15 2010 - 11:30:04 PDT
