[gmx-users] After simulated annealing and then energy minimizing, a docked molecule seems to still be distorted?
aroberts99163 at yahoo.com
Fri Jun 4 06:12:44 CEST 2010
I am doing simulated annealing of a docked molecule. Because of
vibrational modes, the aromatic rings are somewhat distorted. I tried
energy minimization afterwords, but I can't seem to get the
distortions out of the rings. Is there a way to energy minimize, so
that the geometry is correct for the docked molecule? I tried
reducing the emtol a lot (i.e. 0.0001), but this didn't improve things
much. Your help is much appreciated.
Dr. Arthur Roberts, Ph.D.
University of California, San Diego
Skaggs School of Pharmacy and Pharmaceutical Sciences
9500 Gilman Drive #0703
La Jolla, CA 92093-0703
email: aroberts99163 at yahoo.com
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