AMBER Archive (2005)

Subject: Re: AMBER: leap bond angle building

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Feb 08 2005 - 18:00:12 CST

> I'm building a new residue. I do have 3 atoms of a new atom type in
> a planar triangle with a 4th atom of a new atom type of top of it. I get
> the
> following comments in leap. What does this mean? Am I doing something
> wrong or unwanted? Thanks.
>
> --Julie
>
> Building proper torsion parameters.
> 1-4: angle 3 4 duplicates bond ('triangular' bond) or angle ('square' bond)
>
> 1-4: angle 3 4 duplicates bond ('triangular' bond) or angle ('square' bond)
>
> 1-4: angle 2 3 duplicates bond ('triangular' bond) or angle ('square' bond)
 
If you intentionally have atoms bonded in a triangle or square
formation, there's nothing to worry about.

I added these warnings since the situation is detected when building
the 1-4 exclusion list, and those bonding situations are unusual
enough to be possible errors. Probably it should have 'warning' in
front of the msg.

Bill
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