Conformer Plugin

 I am frequently using the Conformer Plugin of Marvin Sketch for 
calculating the possible conformers and also the lowest energy 
conformer of molecules with molecular weight around 150-800 g/mol. 
Afterwards the calculated conformer geometries are used further for 
geometry optimization and UV-Vis spectrum calculations.
 If I am calculating the possible 20 or 50 conformers of the molecule, 
usually more or less the half of these conformers have lower energies 
than the "lowest energy conformer". (Certainly I am using the same 
method for both calculations). Why is this and which geometry has to 
be considered the lowest energy one?

 Thank you for your answer in advance,
 Kind regards,
 Krisztina

Dear Krisztina,

When using "Lowest energy conformer" option a couple of conformers are generated and the one with the lowest calculated energy is returned. A wider conformational analysis can find conformer(s) with lower energy, however your observation indicates a bug around this option. We will notify you in this topic if any progress is made.

Energies calculated during conformational analysis should be considered OK according to the force field used. Note that with other force field(s)/methods the generated conformers are not necessarily represent local/global energy minima.

When using other geometry optimization/higher level calculation methods multiple generated conformers should be optimized and compared.

If you have any further questions then do not hesitate to ask them

Regards,

Gabor