Re: [AMBER] Determining rings in a molecule

From: gilbert <>
Date: Tue, 04 Jan 2011 22:07:30 -0500

 On Tue, 4 Jan 2011 12:57:59 -0800, Bill Ross <ross.cgl.ucsf.EDU> wrote:
>> 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
> _______________________________________________
> AMBER mailing list

 Do a search on SSSR algorithm, Smallest Set of Smallest Rings, which is
 the standard method for finding rings. It has been programed in a number
 of open source packages such as openBabel - and the original Figueras
 code can be found if you look hard enough. A lot depends upon what you
 want and how general you want the code to be, how large a ring system
 you want to deal with.

 Kevin Gilbert
 Serena Software

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