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Isra3l / ligpargen

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ligpargen running problem #2

Closed zhubd11 closed 2 years ago

zhubd11 commented 2 years ago

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 commented 2 years ago

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