> I want to know that is there a way to find out how
> many rings are there in any given molecule (that is coordinates are
> given). To determine which atoms belong to which ring and whether that
> ring is planar or not?
I don't know of any ring-detection abilities in Amber. The topology
file gives the bonds, so you could maybe adapt some graph-theoretic
code to pick out the topological rings, then look at the crds and
analyze planarity. It would be a significant coding effort.
Bill
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Received on Tue Jan 04 2011 - 13:00:02 PST
