Re: [Open Babel] from mol to mop

[Noel O'B. <bao...@gm...>]

This is a question about comp chem not obabel. If you are doing a frequency
calculation (calculation of force constants), then you need to optimise the
geometry first. The frequency calculation and associated thermochemistry is
only valid when the gradient is zero.

- Noel

On 25 April 2012 18:45, Marie-Noelle Pons <
mar...@en...> wrote:

>  Hi
> It is much better. Th heat of formation  is almost the same as in the
> example but the next pb is  :
>           GRADIENT NORM =  35.11809
>
>  ** GRADIENT IS TOO LARGE TO ALLOW FORCE MATRIX TO BE CALCULATED,
> (LIMIT=10) **
>
>  EITHER ADD 'LET' OR REDUCE GRADIENT
>  USING 'TS' OR OTHER GEOMETRY OPTIMIZER
>
> I there something I can do with babel to solve that ?
>
> A+
> MN P
>
>
> Le 25/04/2012 17:29, Noel O'Boyle a écrit :
>
> Hi Marie-Noëlle,
>
>
> What exactly is T.E.S.T.? Google cannot find it.
>
> Without knowing, I'm guessing that you made a 2D structure. MOPAC requires
> a 3D structure. Try using --gen3D to make a 3D structure.
>
> If there is still a problem, it means that OB has gotten the units
> confused, and it's a bug on our end. If that's the case, please send us the
> mol file as an attachment.
>
> - Noel
>
>  On 24 April 2012 14:17, Marie-Noelle Pons <
> mar...@en...> wrote:
>
>> Hi, I am new in using tools such as babel and mopac. I am first running
>> a small test on formaldehyde. I have designed the mol file using
>> T.E.S.T. from US EPA, then used babel to get from .mol to .mop in
>> cartesian units. Now when I run mopac, some atoms are too close one from
>> the other. I cannot see how to modify the distances within babel
>> (obvkously the distances between atoms are smaller than in the mopac
>> example), or is it a pb with T.E.S.T.
>> Thanks for your help
>> MN P
>>
>> --
>> Dr Marie-Noëlle PONS
>> DR CNRS
>>
>> Laboratoire Reactions et Génie des Procédés (LRGP) - CNRS
>> Université de Lorraine
>> ENSIC, 1, rue Grandville BP 20451
>> F-54001 Nancy cedex, France
>>
>> tel: (33) 03 83 17 52 <%2833%29%2003%2083%2017%2052> 77
>> fax: (33) 03 83 32 29 <%2833%29%2003%2083%2032%2029> 75
>> e-mail: Mar...@un...
>>
>>
>>
>>
>>
>>
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>
>
>
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>
> --
> Dr Marie-Noëlle PONS
> DR CNRS
>
> Laboratoire Reactions et Génie des Procédés (LRGP) - CNRS
> Université de Lorraine
> ENSIC, 1, rue Grandville BP 20451
> F-54001 Nancy cedex, France
>
> tel: (33) 03 83 17 52 77
> fax: (33) 03 83 32 29 75
> e-mail: Mar...@un...
>
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> OpenBabel-discuss mailing list
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> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
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>