AMBER Archive (2009)

Subject: Re: [AMBER] Re: COOH troubling

From: Jio M (jiomm_at_yahoo.com)
Date: Wed Dec 09 2009 - 09:01:30 CST

Dear Sir,

>is there a missing hydrogen on O2?

No, it is carbonyl oxygen attached to C13. Also double bond is seen in xleap when mol2 is loaded with GAFF and its frcmod file.

> What is the overall charge?

 it is 0.000001 that is less than permissible error of 0.0006. So it is neutral

>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?

It should be planar(the three ring "planar" system is nearly
perpendicular to single aromatic ring). I optimised structure with
hf/lanl2dz and calculated esp. Then I used gout file for RESP charge
derivation by antechamber

Also in trajectory I can see that even "aromatic" ring made by
C14,C15,C16,C17,C18,C19 also getting distorted. All these carbons have
been assigned type of "ca" by antechamber as it can be seen in mol2
file also.

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

>same behavior

I am trying NOW with acetic acid and will reply as early possible.

thanks and regards;

JIomm

--- On Wed, 12/9/09, case <case_at_biomaps.rutgers.edu> wrote:

From: case <case_at_biomaps.rutgers.edu>
Subject: Re: [AMBER] Re: COOH troubling
To: "AMBER Mailing List" <amber_at_ambermd.org>
Date: Wednesday, December 9, 2009, 1:40 PM

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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