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
