AMBER Archive (2009)

Subject: Re: [AMBER] antechamber bug: output of incorrect bond character

From: case (case_at_biomaps.rutgers.edu)
Date: Wed Sep 02 2009 - 20:53:37 CDT

On Wed, Sep 02, 2009, Matthew Walsh wrote:
>
> I have discovered antechamber outputs the incorrect two incorrect bond
> characters (#35, #36) for the attached molecule as a result of the
> following command:
>
> /usr/local/amber10/exe/antechamber -i ~/test.mol2 -fi mol2 -o out.mol2
> -fo mol2 -c gas -at sybyl -j 4 -pf y -nc 1

Can you be more specific about what you mean by "incorrect bond characters"?
It is treating the sulfur as hypervalent, and this is the most common
representation, although there are other possible Lewis structures. A nice
discussion of the problematic question of S-O bond orders is here:

 http://www.av8n.com/physics/draw-molecules.htm#sec-bogus-methanesulfonic

(or, just Google for "sulfate Lewis dot structure"). One can argue about the
"correct" result, but this page supports the notion that antechamber's
assignment of double bonds to the oxygens is what "almost all references"
would assign.

Note that the bond orders are not used by Amber for anything; it's the bond
lengths and force constants (etc.) that determine the molecular mechanics
representation. So, if you don't like the hypervalent representation of bond
orders, feel free to put some other number in there.

(Apologies if you were really reporting some other problem....)

...dac

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