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Message-ID: <b87c422a0808081437x518f22acyab7960ff2b13bf80@mail.gmail.com>
Date: Fri, 8 Aug 2008 23:37:34 +0200
From: "Francesco Pietra" <chiendarret@gmail.com>
To: "users nwchem" <nwchem-users@emsl.pnl.gov>
Subject: [NWCHEM] Single point energy
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Hi:

I would like to evaluate the relative energies in vacuum for a
flexible, large (100 total atoms) molecule in two ground-state
conformations.

One is the least-strain conformation obtained from molecular mechanics
in vacuum with MMFF94 force field.

The other conformation is what is obtained from docking the molecule
as a ligand onto a protein, followed by molecular dynamics in a
hydrated lipidic bilayer.  The pdb for the ligand can be extracted
from the final pdb. On adapting to the receptor, the molecules
acquires strain, particularly vW strain.

Is that a sound procedure or a "task minimize" is first needed in
order to get reliable indications? At any event, my interest is in
comparing the molecules in the conformations described.

Thanks
francesco pietra