I started using the SD format instead, and it fixed my problems (the
molecules now have correct bond orders and they are MMFF94 optimized
properly).
Thanks for the help!
On Thu, Nov 2, 2017 at 3:21 PM, Paolo Tosco <paolo.to...@unito.it> wrote:
> Hi Patrick,
>
> I don't know Avogadro in detail, but as it is based on OpenBabel I can
> imagine it uses an algorithm to guess bond orders from bond distances,
> angles, etc., whereas the RDKit does not. In fact, if I convert a benzene
> ring from SMILES to SDF through PDB format (which does not contain any bond
> information once CONECT records are removed), I still get correct bond
> orders; this does not happen with RDKit (which is expected):
>
> echo 'c1ccccc1' | babel --gen3d -i smi -o pdb | grep -v CONECT | babel -i
> pdb -o sdf
>
> yields
>
>
> OpenBabel11021718533D
>
> 12 12 0 0 0 0 0 0 0 0999 V2000
> -0.7600 1.1690 -0.0010 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.6330 1.2450 -0.0010 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.3950 0.0770 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.7640 -1.1680 0.0030 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.6290 -1.2430 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.3910 -0.0750 -0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.3540 2.0790 0.0010 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1.1240 2.2140 -0.0030 H 0 0 0 0 0 0 0 0 0 0 0 0
> 2.4800 0.1350 -0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1.3580 -2.0780 0.0060 H 0 0 0 0 0 0 0 0 0 0 0 0
> -1.1200 -2.2130 -0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -2.4760 -0.1340 -0.0030 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0 0 0 0
> 1 7 1 0 0 0 0
> 2 3 2 0 0 0 0
> 3 9 1 0 0 0 0
> 3 4 1 0 0 0 0
> 4 10 1 0 0 0 0
> 5 11 1 0 0 0 0
> 5 4 2 0 0 0 0
> 6 1 2 0 0 0 0
> 6 5 1 0 0 0 0
> 8 2 1 0 0 0 0
> 12 6 1 0 0 0 0
> M END
>
> whereas:
>
> mol = Chem.AddHs(Chem.MolFromSmiles('c1ccccc1'))
> rdDistGeom.EmbedMolecule(mol)
> molFromPDB = Chem.MolFromPDBBlock(re.sub('CONECT.*\n', '',
> Chem.MolToPDBBlock(mol), flags=re.MULTILINE), removeHs = False)
> print (Chem.MolToMolBlock(molFromPDB))
>
> yields
>
>
> RDKit 3D
>
> 12 12 0 0 0 0 0 0 0 0999 V2000
> -0.0060 -1.3620 0.0590 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.2180 -0.7080 0.0690 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.2090 0.6740 -0.0030 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.0030 1.3620 0.0280 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.2210 0.7090 0.0760 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.1960 -0.6780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.0250 -2.4100 -0.2260 H 0 0 0 0 0 0 0 0 0 0 0 0
> -2.1060 -1.1760 0.4870 H 0 0 0 0 0 0 0 0 0 0 0 0
> -2.0910 1.1950 -0.3790 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0420 2.4080 -0.2780 H 0 0 0 0 0 0 0 0 0 0 0 0
> 2.1030 1.1830 0.5000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 2.0960 -1.1980 -0.3330 H 0 0 0 0 0 0 0 0 0 0 0 0
> 2 1 1 0
> 3 2 1 0
> 4 3 1 0
> 5 4 1 0
> 6 5 1 0
> 6 1 1 0
> 7 1 1 0
> 8 2 1 0
> 9 3 1 0
> 10 4 1 0
> 11 5 1 0
> 12 6 1 0
> M END
>
> Note that the RDKit gets the correct bond orders if the PDB file contains
> CONECT records with duplicate (or triplicate) entries for the relevant atom
> indices, which is the widely accepted (though non official) way to encode
> bond orders in PDB files.
>
> Cheers,
> p.
>
> On 11/02/17 18:45, Patrick Avery wrote:
>
> 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::MMFFOptimizeMolec
>> uleConfs().
>>
>> 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
>>
>>
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