AMBER Archive (2004)

Subject: RE: AMBER: How to solve these warnings?

From: Kristina Furse (
Date: Wed Apr 21 2004 - 15:35:57 CDT

I remembered this coming up a couple of years ago--here's a link to Case's

>===== Original Message From Bill Ross <> =====
>> ** Warning: No sp2 improper torsion term for H-H-N3-H
>> atoms are: H1 H2 N H3
>Remembering that the only impropers leap handles are the planar,
>'Y'-shaped variety:
> A B
> \ /
> C
> |
> D
>I wonder why an NH3 group would be seen as a planar 'Y' group.
>Plus I wonder why leap would be complaining about a missing
>improper term, since its algorithm involves silently ignoring
>'Y' configurations that lack improper parameters *unless*
>(as far as I remember having debugged the code in the 90's)
>they involve atoms listed in the IMPROPER section of a prepin
>file loaded in the same session. So I wonder if there is an
>antechamber-generated prepin file involved with an incorrect
>IMPROPER section.
>I'm not up on the latest amber stuff, but no matter how one
>slices it, the warning seems fishy to me.
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Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University

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