On 2012-11-13 12:15, Chris Morley wrote:
> On 12/11/2012 17:50, David van der Spoel wrote:
>> Hi,
>>
>> I have now implemented the extraction of G2/3/4 energies from Gaussian
>> files, e.g.
>>
>> % babel -ig98 water-g3.log.gz -oinchi
>> DHf(0K) = -56.778415 kcal/mol.
>> DHf(298.15K) = -59.838414 kcal/mol.
>> InChI=1S/H2O/h1H2
>> 1 molecule converted
>> 11 audit log messages
>>
>> Now my question is what to do with the result?
>>
>> So far I've used:
>>
>> OBPairData (set attribute and value)
>> OBMol.SetData(PairData)
>>
>> since each calculation yields at least two values (Delta H_form at 0K
>> and 298.15K) this seemed to be the most flexible way. Then
>>
>> OBPairData obpd = OBMol.GetData("DHf(0K)") would get the appropriate
>> data struct from a molecule. Is this a suitable way?
>
> OBPairData is a good place for single items because they can be
> automatically output as properties in sdf or cml files (without
> programming).
Cool, that works instead.
> <GXmethod>
G4
> <DHf(0K)>
-56.694956
> <DHf(298.15K)>
-59.754956
>
> It would also be possible to make a descriptor DHf(T) with T as a
> parameter, although I doubt this is of sufficiently general interest.
>
In practice we don't have experimental data at any other T than 298.15K
which makes it difficult.
> Is the code available?
>
Soon. I'm also including ESP points with new class based on OBGrid, but
for this I need to find out how to add an instance of OBGrid to a molecule.
> Chris
>
>
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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