Thanks for the information!
Take care,
Sam
On Wed, May 27, 2015 at 3:44 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Wed, May 27, 2015 at 4:07 PM, Samuel Bowerman <
> sbowerma+amber-l.hawk.iit.edu> wrote:
>
> > Hi Jason,
> >
> > Thanks for the response. Perhaps you could enlighten me as to what part
> of
> > the calculation is inherently explicit? For example, if I want to
> analyze
> > the specific interaction of a ligand with a small subsection of the
> binding
> > protein, I define two groups: "ligand" and "subset (surroundings)". How
> > does explicit vs implicit matter for this case if I am only calculating
> > pair-wise point-charge energies for these groups? If I were to define
> only
> > the ligand group, then the surroundings would include the explicit
> waters,
> > but that may not always be the case, correct?
>
>
> As I understand it, LIE is usually a difference between ligands
> interacting in different environments -- the solvated protein and in
> solution surrounded by water molecules. So you usually run two different
> explicit solvent simulations - one of the isolated ligand in solution and
> one of the ligand in its protein environment (in solution), and the
> difference is scaled linearly, usually with separate scaling factors for
> electrostatics and van der Waals.
>
> You may be able to apply this approach in an implicit solvent environment,
> but that would require GB or something of the like -- a simple dielectric
> scaling isn't going to do the same thing.
>
> All the best,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed May 27 2015 - 15:00:02 PDT
