ligpargen running problem

[zhubd11]

I tried with BOSS 4.9 and ligpargen compiled with conda python3.7, but when I run it, I get this error, below are the error output:

ligpargen -i part2.pdb -n phenol -p phenol -r MOL -c 0 -o 0 -cgen CM1A
[16:59:22] Explicit valence for atom # 25 O, 5, is greater than permitted
Traceback (most recent call last):
File "/public1/home/scb1100/miniconda3/envs/test/bin/ligpargen", line 33, in
sys.exit(load_entry_point('LigPargen', 'console_scripts', 'ligpargen')())
File "/public1/home/scb1100/ligpargen/ligpargen-main/ligpargen/ligpargen.py", line 494, in main
molname=args.molname, workdir= args.path, debug= args.debug)
File "", line 17, in init
File "/public1/home/scb1100/ligpargen/ligpargen-main/ligpargen/ligpargen.py", line 174, in post_init
moleculeRDkit, newIndexToOriginalIndex, atomsNameOriginal, residueNameOriginal = utilities.generateRDkitMolecule(self.ifile, self.smile, self.workdir, molnameA, self.debug)
File "/public1/home/scb1100/ligpargen/ligpargen-main/ligpargen/tools/utilities.py", line 165, in generateRDkitMolecule
atomsIndexLstWithRightOrder = buildProperOrderAtomIndexLst(molecule, molname, workdir)
File "/public1/home/scb1100/ligpargen/ligpargen-main/ligpargen/tools/utilities.py", line 513, in buildProperOrderAtomIndexLst
heavyAtomsIndexLst = [atom.GetIdx() for atom in molecule.GetAtoms() if atom.GetSymbol() != 'H']
AttributeError: 'NoneType' object has no attribute 'GetAtoms'

Any ideas？

[Isra3l]

Hey zhubd11!

By default, BOSS checks the molecule integrity as a sanity check of the inputs. Probably your input PDB (part2.pdb) has something wrong (atoms too close, wrong charge, ...). You should take a look in pymol/chimera/VMD/... and see where is the problem.

Good luck!

Israel