> anyone would advise changes. Am I right in saying that the mol is updated to
> the best conformer and this is what will be written to the output file?
Yup. This is very similar to my version of this -- I usually usually something
like:
ff.SteepestDescent(1500, 1.0e-4)
ff.WeightedRotorSearch(250, 25)
ff.ConjugateGradients(2500, 1.0e-6)
ff.GetCoordinates(mol)
This way, there's a quick cleanup before searching, and a longer clean-up
afterwards.
> One thing I notice with a calculation, was that the lowest energy did not
> match any of the conformer energies (see below). Is this an error?
This likely means the initial (step 0) conformation was lowest in energy.
Hope that helps,
-Geoff
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