Re: [AMBER] Determining rings in a molecule

From: manoj singh <>
Date: Sat, 1 Jan 2011 16:49:35 -0500

On Sat, Jan 1, 2011 at 4:51 AM, Pooja Khurana <> wrote:

> 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?

Not unless topology of that molecule is defined in AMBER.

> 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?

Assignment of atom types provided the file is in MOL2 format (or other
format with connect information)

> 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.

Most of the visualizers form bonds based on the distances between atoms.

> I would be really grateful if i can get a reply for this.
> Thanks
> in advance,
> Regards,
> Pooja
> B.E. Biotechnology
> India
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Received on Sat Jan 01 2011 - 14:00:02 PST
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