[Rdkit-discuss] UFF atom type errors

[Bennion, B. <ben...@ll...>]

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