AMDock
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Valdes-Tresanco-MS
error with prepare_receptor4
i have a protein with some of the coordinates looks like this: ATOM 5063 CG LYS B 316 157.454-100.044 -4.756 0.0187 1.9080 as you notice the X and Y coordinates are not separated by space. when i tried to run the prepare_receptor4 in AMDock it produced this error:
Traceback (most recent call `last):
File "/home/ibrahim/anaconda3/envs/AMDock/lib/python3.9/site-packages/MolKit/pdbParser.py", line 433, in parse_PDB_atoms
at = self.parse_PDB_ATOM_record(atRec, mol)
File "/home/ibrahim/anaconda3/envs/AMDock/lib/python3.9/site-packages/MolKit/pdbParser.py", line 1375, in parse_PDB_ATOM_record
atom._coords = [[float(rec[5]), float(rec[6]), float(rec[7])]]
ValueError: could not convert string to float: '157.454-100.044'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/ibrahim/anaconda3/envs/AMDock/lib/python3.9/site-packages/AMDock/command_runner.py", line 64, in run
result = self.fn(*self.args)
File "/home/ibrahim/anaconda3/envs/AMDock/lib/python3.9/site-packages/AMDock/tools.py", line 499, in __init__
self.pqr = Read(pqr_file)[0]
File "/home/ibrahim/anaconda3/envs/AMDock/lib/python3.9/site-packages/MolKit/__init__.py", line 74, in Read
molecules = parser.parse()
File "/home/ibrahim/anaconda3/envs/AMDock/lib/python3.9/site-packages/MolKit/pdbParser.py", line 653, in parse
self.pdbRecordParser[record](self.allLines, self.mol)
File "/home/ibrahim/anaconda3/envs/AMDock/lib/python3.9/site-packages/MolKit/pdbParser.py", line 437, in parse_PDB_atoms
raise RuntimeError("Error parsing the following line in pdb:\n" + atRec)
RuntimeError: Error parsing the following line in pdb:
ATOM 5063 CG LYS B 316 157.454-100.044 -4.756 0.0187 1.9080
set verbose to True
set cleanup to nphs_lps_waters_nonstdres_deleteAltB
Traceback (most recent call last):
File "/home/ibrahim/anaconda3/envs/AMDock/lib/python3.9/site-packages/AutoDockTools/Utilities24/prepare_receptor4.py", line 157, in <module>
mols = Read(receptor_filename)
File "/home/ibrahim/anaconda3/envs/AMDock/lib/python3.9/site-packages/MolKit/__init__.py", line 38, in Read
raise AssertionError("%s does't exist" % filename)
AssertionError: HIF_pymol_h.pdb does't exist
fixed via https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3/commit/eacca6e92b9064639bce44c54a7db1ada7be9d77 Please, update AutoDockTools:
python -m pip install git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3 -U
Linux 64-bit Ubuntu 20.04> Autodock Vina > "Prepare input" returns the following error: Unhandled Python exception Aborted (core dumped)
@RashedCh I need more information. Can you attach an image of the program log where I can see the error?
Hi Mario, thanks for getting back to me.
Here's what I tried - [image: image.png]
When I "Prepare Input", the program crashes with the following error msg:
[image: image.png]
Best, Rashed
On Sat, Jun 18, 2022 at 8:55 PM Mario Sergio Valdés Tresanco < @.***> wrote:
@RashedCh https://github.com/RashedCh I need more information. Can you attach an image of the program log where I can see the error?
— Reply to this email directly, view it on GitHub https://github.com/Valdes-Tresanco-MS/AMDock/issues/18#issuecomment-1159611048, or unsubscribe https://github.com/notifications/unsubscribe-auth/APBFK7WKQ6O7LC4TB74JPMTVP2KZ3ANCNFSM5OXVLS3Q . You are receiving this because you were mentioned.Message ID: @.***>
Please upload the images again because they are not visible. The program log is shown on the right side.
The program closes down completely leaving an error the following error on the terminal
fixed via https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3/commit/aee55d50d5bdcfdbcd80220499df8cde2a8f4b2a Please, update AutoDockTools:
python -m pip install git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3 -U