Description
Hello,
when I ran "Parameterise ligand with Gasteiger charges", there was a FileNotFoundError :
`/bin/bash: line 1: 111355 Segmentation fault (core dumped) mk_prepare_ligand.py -i /content/6LQA/LIGAND/BBR.sdf -o /content/6LQA/DOCKING/BBR/BBR.pdbqt > /dev/null 2>&1
FileNotFoundError Traceback (most recent call last)
in <cell line: 28>()
26 #else:
27 #print(f"Error: The file {LIG_pdbqt_dFFile} does not exist.")
---> 28 pdbqt_add_chid(LIG_pdbqt_dFFile)
29
30 print(f'+ Parameterisation: {LIG_sdf} > {LIG_pdbqt}')
in pdbqt_add_chid(inpt_file)
5
6 def pdbqt_add_chid(inpt_file: str) -> None:
----> 7 with open(inpt_file, 'r') as inpt:
8 data = inpt.read()
9 new_data = data.replace(' UNL ', ' UNL A')
FileNotFoundError: [Errno 2] No such file or directory: '/content/6LQA/DOCKING/BBR/BBR.pdbqt'`
I tried
!mk_prepare_ligand.py -i {LIG_sdf_lFile} -o {LIG_pdbqt_dFFile} if os.path.exists(LIG_pdbqt_dFFile): pdbqt_add_chid(LIG_pdbqt_dFFile) else: print(f"Error: The file {LIG_pdbqt_dFFile} does not exist."), and there indeed doesn't exist. I only have folder "'/content/6LQA/DOCKING/BBR"
Could you please help me out that what am I doing wrong here? Is my system path have no “mk_prepare_ligand.py”？
Appreciate for your guide！