Re: [AMBER] leap mis-specified improper dihedral

From: David A Case <>
Date: Tue, 20 Dec 2011 15:18:17 -0500

On Tue, Dec 20, 2011, Dean Cuebas wrote:
> I am to understand that the improper is specified as (Y-Y-X-Y) on an sp2
> hybridized center where X is the sp2 center atom.
> When I ran xleap, I obtain an improper that is (Y-X-Y-Y) where all the
> atoms are correct, except the sp2 center is in the second position of the
> specified dihedral.

This is OK: a dihedral angle is unchanged when you reverse the order of the

> Also, I notice that in a heteroaromatic fused ring system like adenine,
> the impropers are only assigned to sp2 centers that have an exocyclic
> substituent, and NOT the bridging aromatic sp2 centers.

This was a choice made way back when (1985 or so) because vibrational
modes for the fused systems in purines and tryptophan did not appear to
require additional improper terms on the bridging carbons. I don't know
that this is a general rule for all fused systems, so you might want to
consider trying some different models.


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Received on Tue Dec 20 2011 - 12:30:02 PST
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