using MarvinSketch and are very impressed with its ease of use and
broad functionality. I have two questions related to the Conformers
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?
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
Thanks very much for your help.