AMBER Archive (2008)

Subject: AMBER: distorted aromatic rings

From: Marc Lindner (nightfly21_at_gmx.de)
Date: Wed Jan 23 2008 - 04:40:20 CST

I have problems to keep aromatic rings flat. Using the forcefields 99SB and 03 all aromatic rings of the protein and the ligand get distorted. The input preparation with antechamber (gaff) for the ligand and with xleap/ff03 for the protein causes no warnings for bonds, angels and torsions (just few close contacts in the protein and a non-zero charge). While saveamberparm the message appears: total 15 improper torsions applied (ligand); total 799 improper torsions applied (protein).

I read the related FAQs, how to keep aromatic rings flat, but I did not understand the answer. Are missing impropers causing this problem? And where can I find these lacking impropers, especially for the protein? The distortion occurs already during the initial minimization and gets more pronounced during equilibration and molecule-dynamic.

Marc Lindner 

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