AMBER Archive (2009)

Subject: Re: [AMBER] GAFF conjugated ring system dihedrals

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu Jan 29 2009 - 12:37:24 CST

On Wed, Jan 28, 2009, Floris Buelens wrote:
>
> I have a question relating to the molecule attached (once with GAFF and
> once with sybyl atom types in mol2 format). Specifically I'm looking
> at the two bonds, formally single, that link the maleimide (5-membered
> ring) to the two indole groups....
>
> Can anyone provide some insights into whether this is representative of
> the physical reality, or if this could be an artifact resulting from the
> linking of two conjugated ring systems?

Generically, you should be suspicious of antechamber results with linked
conjugated ring systems, and partial double bonds. Use what you get
either with caution, or as a starting point for developing your own
parameters (say by comparisons to quantum results). But I don't have
any specific experience (good or bad) to cite here.

...dac

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber