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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