AMBER Archive (2004)

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

From: Bill Ross (
Date: Wed Apr 21 2004 - 13:21:30 CDT

> ** 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
    \ /

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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