[AMBER] Determining rings in a molecule

From: Pooja Khurana <btpooja.yahoo.in>
Date: Sat, 1 Jan 2011 15:21:14 +0530 (IST)

Hi everyone,

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 was going through the paper of
antechamber in which it was mentioned that the assignment is done to the
 atoms belonging to ring structure and depending on their aromaticity.
But can I get the path of the linked atoms?

For example, lets say
 in the pdb i have 10 atoms, out of which 5 are forming a ring structure
 when i visualize that in a viewer. Now can i determine without using
the viewer which all atoms are connected in a ring C1-C2-C6-C5-C7-C1.
Something like this? Similarly if there are two ring structures, then i
get two such strings.

I would be really grateful if i can get a reply for this.

 in advance,

B.E. Biotechnology

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Received on Sat Jan 01 2011 - 02:00:02 PST
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