AMBER Archive (2009)

Subject: Re: [AMBER] Re: COOH troubling

From: case (case_at_biomaps.rutgers.edu)
Date: Wed Dec 09 2009 - 07:40:10 CST

On Wed, Dec 09, 2009, Jio M wrote:
>
>
> b) ALSO all the rings are distorted and I think rings are behaving as Cyclohexane.

You have a very weird molecule here: is there a missing hydrogen on O2? What
is the overall charge? It may well be that antechamber doesn't know the right
thing to do with the environment around O1. Are you sure that your ligand
is indeed a planar system?

For the COOH behavior, test things out on a simple acid to see if you get the
same behavior.

...good luck....dac

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