Dear Patrick,

my guess is that you loaded the caffeine coordinates from PDB, or anyway from a format where bond orders were not specified. All atoms appear to be sp3-hybridized, which results in the wrong geometry being generated.


Hope that helps,
Paolo


On 11/02/17 18:20, Patrick Avery wrote:
Hey there RDKitters,

I have been generating conformers in RDKit, optimizing them using MMFF94, and sorting them by their energies. For some tests, I have been using caffeine. But I seem to have some strange results, and I wonder if anyone knows why.

I have attached two images of an MMFF94 optimized caffeine conformer. In them, the oxygen in the top right corner is the primary strange thing I see (although it doesn't seem to be very planar either, which may be somewhat strange).

Note that the oxygen is sticking out of the plane of the molecule. This is the lowest energy conformer generated and optimized by RDKit (and other conformers low in energy are similar to it - with the oxygen sticking out).

If I take that exact molecule and MMFF94 optimize it in Avogadro, all the atoms move to be in the same plane (including the oxygen that was sticking out). So the problem goes away if I MMFF94 optimize it with Avogadro.

So the question is: why are RDKit and Avogadro giving different results for the MMFF94 optimization? And why does RDKit's MMFF94 push the oxygen out of the plane so much?

In RDKit, I am using the C++ function RDKit::MMFF::MMFFOptimizeMoleculeConfs().

My parameters are the mol (with all the conformers in it), an empty result vector, 1 thread, 1000 maximum optimization iterations, "MMFF94" for the mmffVariant, 100.0 for the nonbonded threshold, and true for ignoreInterfragInteractions.

Let me know if anyone knows why.

Thanks,
Patrick


------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot


_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Reply via email to