On Sun, Oct 23, 2011, Anglea A. wrote:
> How can I include polarization term in the energy calculation (Epol=−2∑iμi· Eio)?
You need to use a polarizable force fields (e.g. leaprc.ff02pol.r1), and set
ipol=1 in the sander input file.
Please note that, for now, all of the polarizable force fields in Amber are
rather old, and have not been extensively tested. New polarizable versions
will be released soon, but please don't assume that the current polarizable
versions are "better" than non-polarizable force fields.
> Does it mean, once I use lone pair on my ligand, the energy equation
> will automatically include the polarization term? or I need to use a
> keyword?
There is no connection between lone pairs and polarizability. Note that
if you wanted a polarizable force field for a ligand, you would have to
create the appropriate files yourself from scratch. Built-in polarizable
potentials are only available for proteins and nucleic acids. Making such
files for ligands is a *very* advanced topic, such that you should be the
person answering questions about polarizable force fields, not asking them. :-)
[There is also the possibility of using Amoeba polarizable potentials, which
can be done for ligands as well as proteins. Amber has some limited support
for this, but you should consult the amoeba papers for details.]
....dac
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Received on Tue Oct 25 2011 - 06:00:02 PDT
