AMBER Archive (2004)

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

From: Bill Ross (ross_at_cgl.ucsf.edu)
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
    \ /
     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.

Bill
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