AMBER Archive (2004)

Subject: RE: AMBER: Xleap crash, problem with residue bonding

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Jul 22 2004 - 16:55:58 CDT

> 1-4: angle 76 192 duplicates bond ('triangular' bond) or angle
> ('square' bond)
> ...
> So it seems that xleap thinks there are problems with certain angles
> duplicating bonds that form a triangle (I guess).

I think this means there are bonds forming triangles or squares.

1-4 interactions are treated seperately for nb calcs because it
is assumed that bond/angle/torsion terms cover those interactions.
As far as I remember, these cyclical structures are detected when
building excluded atom lists from bond and angle (and dihedral?)
lists.

Bill
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