Yes, that is probably correct. I am loading a pdb file for the initial
conformer, so bond orders are not specified.
But I find it strange, still, that when I use MMFF94 in Avogadro to
optimize it, it results in a planar shape even though all the bonds are
still single.
On Thu, Nov 2, 2017 at 2:38 PM, Paolo Tosco <paolo.to...@unito.it> wrote:
> 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
> listRdkit-discuss@lists.sourceforge.nethttps://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
>
>
------------------------------------------------------------------------------
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
