Questions about Conformers tool

Dear ChemAxon,

We’re
using MarvinSketch and are very impressed with its ease of use and
broad functionality. I have two questions related to the Conformers
tool:

 

1)      For
many of the molecules we are exploring, if we generate (for example) 10
conformers, we find that several of the conformers have lower energies
than the energy of the single conformer obtained when we select the
“Calculate lowest energy conformer” option. In some cases, the
differences are rather large. What is the explanation for this?

2)      Can
you share details about the algorithm used to generate conformers? I am
familiar with the work of Mekenyan et al (“Conformational coverage by a
genetic algorithm: saturation of conformational space”, J. Chem. Inf.
Model. 2007, 47, 851-863). Does the Conformer tool in MarvinSketch do
something similar? Are there ways to approximate how many conformers
should be generated in order to adequately cover the attainable
conformational space?

 

Thanks very much for your help.

Regards,

Jim

Dear Jim,

Sorry for the late answer.

1)      For many of the molecules we are exploring, if we generate (for example) 10 
 conformers, we find that several of the conformers have lower energies 
than the energy of the single conformer obtained when we select the 
“Calculate lowest energy conformer” option. In some cases, the 
differences are rather large. What is the explanation for this?

It seems to be a bug, needs checkup. Thanks for mentioning it.

2)      Can you share details about the algorithm used to generate conformers?

A brief description of the used method available at http://www.chemaxon.com/library/advanced-automatic-generation-of-3d-molecular-structures/ (see downloadable pdf file: http://www.chemaxon.com/conf/Advanced_automatic_generation_of_3D_molecular_structures.pdf ).

If you have further questions do not hesitate to ask them,

Regards,

Gabor

Thanks for the reply. This certainly seems
like a rather serious bug for those of us using the Conformers tool.
Hopefully it can be fixed soon.

Regards,
Jim

Dear Jim,

 

As replied in https://www.chemaxon.com/forum/viewpost36832.html#36832 a bug was identified; thanks again for reporting. I will close this topic and continue discussion in the linked one.

 

Regards

Gabor