AMBER Archive (2009)

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

From: Matthew Walsh (walshmj_at_purdue.edu)
Date: Wed Sep 02 2009 - 23:30:04 CDT

More specifically, the error is two S=O bounds being represented as
single bonds. I have not been able to find any chemists that do not
disagree with this result.

On Wed, Sep 2, 2009 at 9:53 PM, case<case_at_biomaps.rutgers.edu> wrote:
> 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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