Hello Greg,
The only thought I had was that these atom types just didn’t exist in the UFF
forcefield and therefore I was just out of luck for compounds with boron
(borax) and such.
If there are indeed plausible atom types and rdkit is just not picking them,
then that is another issue all together.
Brian
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: Friday, October 06, 2017 10:27 PM
To: Bennion, Brian <benni...@llnl.gov>
Cc: Guillaume GODIN <guillaume.go...@firmenich.com>; RDKit Discuss
(rdkit-discuss@lists.sourceforge.net) <rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] UFF atom type errors
Yeah, those atom types that you are seeing are the names of the UFF atom types
that the RDKit assigns.
If an atom has a hybridization/charge-state that's not recognized, you'll get
those parameterization errors.
If you're aware of a better way to handle this (or a way to sensibly guess
parameters), please let me know.
-greg
On Fri, Oct 6, 2017 at 8:52 PM, Bennion, Brian
<benni...@llnl.gov<mailto:benni...@llnl.gov>> wrote:
CHEMBL1796997 is Helium and the same molecule that throws the first UFFTYPER
warnings. Originally I had searched my sdf file only for He1 and found no
hits.
From the original Goddard paper in 1992, there is only He4+4 atomtype described
explicitly. I can reason based on the error that RDKIT is classifying He as
He1 and then as He for which there is no formal UFF atom type.
Is this presumption correct?
Brian
From: Guillaume GODIN
[mailto:guillaume.go...@firmenich.com<mailto:guillaume.go...@firmenich.com>]
Sent: Thursday, October 05, 2017 22:59
To: Bennion, Brian <benni...@llnl.gov<mailto:benni...@llnl.gov>>; RDKit Discuss
(rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>)
<rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>>
Subject: RE: UFF atom type errors
Hello,
Can you provide a small sdf contains molecules that have this issue ?
thanks in advance,
BR,
Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
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________________________________
De : Bennion, Brian <benni...@llnl.gov<mailto:benni...@llnl.gov>>
Envoyé : vendredi 6 octobre 2017 06:11
À : RDKit Discuss
(rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>)
Objet : [Rdkit-discuss] UFF atom type errors
Hello,
As part of my workflow, I am attempting to generate a starting 3D structure
from a 2D representation loaded from an sdf file.
On certain structures I receive the following UFF errors when attempting to
minimize the structure.
[20:50:43] UFFTYPER: Unrecognized atom type: He1 (0)
[20:50:43] UFFTYPER: Unrecognized atom type: He (0)
[20:50:45] UFFTYPER: Unrecognized atom type: B_1 (0)
[20:50:45] UFFTYPER: Unrecognized atom type: B_1 (7)
[20:50:45] UFFTYPER: Unrecognized atom type: B_1 (0)
[20:50:45] UFFTYPER: Unrecognized atom type: B_1 (7)
I have searched for these atom labels in my 2D sdf file and they don’t exist.
So I am not sure how the uff code in rdkit is finding these types.
The relevant code is shown below, in case I am doing something incorrectly.
Any thoughts or suggestions to help me find my mistakes?
Brian
for m in ms:
#add hydrogen atoms to the molecule before generating 3D coordinates
mHs=Chem.AddHs(m)
#start generating 3D coordinates and optimize the conformation
embedError=AllChem.EmbedMolecule(mHs,useRandomCoords=True)
if embedError == 0 :
UffoptError=AllChem.UFFOptimizeMolecule(mHs,3000)
elif UffoptError != 0 :
print ("UFF optimization failed, trying MMFF optimization")
MMFFoptError=AllChem.MMFFOptimizeMolecule(mHs,3000)
elif MMFFoptError != 0 :
print ("MMFF optimizaiton has also failed on: ", molName)
print ("Continuing on to next molecule")
continue
else:
print("Embedding Failed for: ", molName)
continue
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