AMBER Archive (2004)

Subject: AMBER: water as a "ligand" in GBSA and MM-PBSA?

From: Giulio Rastelli (
Date: Fri Feb 06 2004 - 11:41:50 CST

Dear all,
I would be interested in estimating the dG of binding of six
different water molecules that solvate a protein binding site.
I though that using GBSA and MM-PBSA would be of
interest. One way to do this in amber7 would be to treat each water
one at a time, as if it was a "ligand", and then determine the deltaG
between complex-(receptor+ligand), where the complex contains the
receptor plus six waters.
Treating explicit water molecules as "ligands" would violate the way in
which solvation energies are calculated in GBSA and MM-PBSA, e.g. with
the continuum approach? Would these calculations make sense?....
Many thanks for your comments


Giulio Rastelli Dipartimento di Scienze Farmaceutiche Universita di Modena e Reggio Emilia Via Campi 183 41100 Modena - ITALY ------------------------------------- tel 0039-059-2055145 fax 0039-059-2055131 -------------------------------------

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