AMBER Archive (2008)

Subject: Re: AMBER: distorted aromatic rings

From: David A. Case (case_at_scripps.edu)
Date: Wed Jan 23 2008 - 10:24:15 CST

On Wed, Jan 23, 2008, Marc Lindner wrote:

> 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).

How non-planar are they? You can visually see distortions in MD simulations,
since only the average structure is truly planar. So, it's not clear whether
you are seeing something that is incorrect, or just something that is
surprising.

...dac

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