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Valdes-Tresanco-MS / AMDock-win

(Windows) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina
GNU General Public License v3.0
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PDB2PQR Problem #14

Closed spmolnar closed 2 years ago

spmolnar commented 2 years ago

Debian Bullseye. Installed in conda env, no warning or error messages.

Test docking of Biotin in Streptavidin (1STP) - vina failed withPDB2PQ finalized with exit code 1 and existstatus 0.

Welcome to AMDock Version 1.6.2 For Windows and Linux

AMDOCK: Defining Initial Parameters... AMDOCK: DOCKING_PROGRAM: AutoDock Vina AMDOCK: WDIR: /home/comp/Apps/Models/1-Streptavidin/AMDTest052622/Biotin AMDOCK: MODE: SIMPLE AMDOCK: TARGET: apo-1stp AMDOCK: TARGET (Hetero): None AMDOCK: TARGET (Zn atoms): None AMDOCK: LIGAND: BTN AMDOCK: LIGAND (heavy_atoms): 15 AMDOCK: Defining Initial Parameters... Done AMDOCK: Prepare Initial Files... AMDOCK: Running PDB2PQR for Target...

INFO:PDB2PQR v3.4.1: biomolecular structure conversion software. INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO:Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO:Checking and transforming input arguments. INFO:Loading topology files. INFO:Loading molecule: /home/comp/Apps/Models/1-Streptavidin/AMDTest052622/Biotin/input/apo-1stp.pdb Traceback (most recent call last): File "/home/comp/Miniconda3/envs/AMDock/bin/pdb2pqr30", line 10, in sys.exit(main()) File "/home/comp/Miniconda3/envs/AMDock/lib/python3.9/site-packages/pdb2pqr/main.py", line 820, in main if main_driver(args) == 1: File "/home/comp/Miniconda3/envs/AMDock/lib/python3.9/site-packages/pdb2pqr/main.py", line 757, in main_driver pdblist, is_cif = io.get_molecule(args.input_path) File "/home/comp/Miniconda3/envs/AMDock/lib/python3.9/site-packages/pdb2pqr/io.py", line 459, in get_molecule pdblist, errlist = pdb.read_pdb(input_file) File "/home/comp/Miniconda3/envs/AMDock/lib/python3.9/site-packages/pdb2pqr/pdb.py", line 2590, in read_pdb raise details File "/home/comp/Miniconda3/envs/AMDock/lib/python3.9/site-packages/pdb2pqr/pdb.py", line 2579, in read_pdb obj = klass(line) File "/home/comp/Miniconda3/envs/AMDock/lib/python3.9/site-packages/pdb2pqr/pdb.py", line 560, in init self.serial = int(line[6:11].strip()) ValueError: invalid literal for int() with base 10: 'HETAT'

Valdes-Tresanco-MS commented 2 years ago

HETAT is not a PDB format keyword, it is probably HETATM. Please check that your file is consistent.

spmolnar commented 2 years ago

Solved.

Have you given any further consideration to implentation of Vina-1.2.3?

On 05/26/2022 07:53 PM, Mario Sergio Valdés Tresanco wrote:

HETAT is not a PDB format keyword, it is probably HETATM. Please check that your file is consistent.

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Valdes-Tresanco-MS commented 2 years ago

Yes, we will try to implement it as soon as possible, but it will take some time since we don't have time or funding for this project, so we work on it in our spare time (which is quite little).

I will close this issue since it was resolved. If you want, you can open a new one with the request for the new implementation