[gmx-users] After simulated annealing and then energy minimizing, a docked molecule seems to still be distorted?

[Arthur Roberts]

Hi, All,

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.

Art

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
cell: 206-850-7468
skype=aroberts92122