AMBER Archive (2009)

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

From: Matthew Walsh (walshmj_at_purdue.edu)
Date: Thu Sep 03 2009 - 10:15:00 CDT

Hello,

The bonds in question are S1-O2 and S1-O3

    35 21 20 1
    36 22 20 1

AmberTools 1.0 was compiled with g95 on Red Hat EL5

On Thu, Sep 3, 2009 at 7:26 AM, case<case_at_biomaps.rutgers.edu> wrote:
> On Thu, Sep 03, 2009, Matthew Walsh wrote:
>
>> 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.
>
> OK.  Then I cannot reproduce your result, I think.  Can you post the out.mol2
> file?  When I run this, I get a bond order of 2 for the S=O bonds in your
> example. Which version of AmberTools, compiler and OS?
>
> ....dac
>
>
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  • application/octet-stream attachment: test.mol2

  • application/octet-stream attachment: out.mol2

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