AMBER: ligand slips out of pocket

From: Hannes Wallnoefer <>
Date: Fri, 4 Apr 2008 09:58:29 +0200


Im modeling a complex with ligand who has two main interaction points. The
first is a cation-pi interaction and the second is a halogen-aromatic
interaction. When running MD Simulation (i used resp HF/6-31G* for the
electrostatic parametrization of the ligand) with Amber 9 my ligand always
"slips" out of the binding pocket. I tried several extensive minimizations and
several ways to equilibrate the system, but nothing fixed the problem. My
question is: Is there another description of the mentioned interaction despite
the coulomb term in the forcefield? And if no, whats the best way to add them
(possibly a distance restraint, but how can I represent the energetic situation

Thanks in advance,
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Apr 18 2008 - 21:16:47 PDT
Custom Search