According to my experience it seems that when GB is 1, the MM part in
the script is ignored; since whatever I change (dial =2, 4,...) the
result for the calculation in vacuum was always the same ???
Antonija
Citiram case <case.biomaps.rutgers.edu>:
> 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 Mon Oct 18 2010 - 02:00:02 PDT
