Please integrate AutoDock Vina v-1.2.3 in AMDock.

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'

when using autodock4 in scoring, it calculates the Unbound System's Energy but it appears as zero at the end... check why is this happening

same error happens when using Linux version and the *.amdock file is empty...

Welcome to AMDock
Version 1.5.2 For Windows and Linux

AMDOCK: Opening AMDock File (*.amdock)...
AMDOCK: Opening AMDock File (*.amdock)... Done.
AMDOCK: Traceback (most recent call last): 
AMDOCK: File "D:\Programs\AMDock-win-master\AMDock-win-master\lib\site-packages\AMDock\result_tab.py", line 176, in load_file 
AMDOCK: 
AMDOCK: self.amdock_load() 
AMDOCK: File "D:\Programs\AMDock-win-master\AMDock-win-master\lib\site-packages\AMDock\result_tab.py", line 188, in amdock_load 
AMDOCK: 
AMDOCK: self.data = self.AMDock.loader.load_amdock_file() 
AMDOCK: File "D:\Programs\AMDock-win-master\AMDock-win-master\lib\site-packages\AMDock\file_loader.py", line 269, in load_amdock_file 
AMDOCK: 
AMDOCK: if os.path.exists(self.AMDock.project.WDIR): 
AMDOCK: File "D:\Programs\AMDock-win-master\AMDock-win-master\lib\genericpath.py", line 26, in exists 
AMDOCK: 
AMDOCK: os.stat(path) 
AMDOCK: TypeError
AMDOCK: : 
AMDOCK: coercing to Unicode: need string or buffer, NoneType found
AMDOCK: 

I made all steps sequentially but when I click on the run button, nothing happens (no error messages are shown and the state does not change)

Hello! Really appreciate what you are doing, after spending far too many hours troubleshooting my way through running AutoDock&vina.

AutoDock vina runs fine for me and I am just going through the simple AutoDock4 docking procedure. Setting up the project, target and ligand, preparing input and automatic search space definition all work fine.

But when I try to run AutoDock, progress gets to about 10.0% (completing the grid maps successfully) before python just starts spitting out a neverending list of IO errors to do with not being able to find the .dlg output file:

AMDOCK: Traceback (most recent call last):
AMDOCK: File "C:[PathToAMDock]\AMDock-win-master\lib\site-packages\AMDock\input_tab.py", line 2164, in autodock_output
AMDOCK:
AMDOCK: ADout = open(self.ADout_file)
AMDOCK: IOError
AMDOCK: :
AMDOCK: [Ernno 2] No such file or directory: 'C:\[PathToProject]\results\CoA_LsAAE3_5ie0_out.dlg'

That file is indeed missing, but a file 'CoA_LsAAE3_5ie0_01.dlg' is in that directory (with some contents).

That error message gets repeated over and over again until I cancel it and the run does not make any further progress.

This happens with various ligand files going in.

Is this an error you have encountered before?
Cheers,
Peter

when processing cytochrome P450, heme group is deleted. The heme group doesn't appear in the AMBER force field. It's necessary to specify CHARMM force field for PDB2PQR

change HEME name in CHARMM.DAT file to HEM (as appear in the PDB)

-Add the option in the program settings.
-Autodetect the ligand atoms types.

I'm wondering if there is an option to make AMDock automatically dock multiple ligands after each other with Autodock4Zn. I'm going to dock 200 ligands and I don't want to start a new project and check all the boxes and everything with every new ligand since that would take forever. Is there any way to do this?

Kind regards,

Victor Hellgren
MSc in Organic Chemistry, Uppsala University

Hi,
I think there is a problem with browsing the different directories.
Clicking the folder to enter into different directories is not possible. Please have a look at this.

I followed the process of Chain:Residue1:Number1; Chain:Residue2:Number2. Also the spelling of Analize results is Analyze

I want to do docking using cyclodextrin and molecule, without using protein. Can you please tell me if it can be done somehow? Because if I load cyclodextrin into the Target field, the program gives an error.

Error message:
AMDOCK: NEW PROJECT...
AMDOCK: Defining Initial Parameters...
AMDOCK: DOCKING_PROGRAM: AutoDock4
AMDOCK: WDIR: C:\Users\alexa\Desktop\AMDock\new2
AMDOCK: Traceback (most recent call last):
AMDOCK: File "C:\Users\alexa\Downloads\AMDock-win-master\AMDock-win-master\lib\site-packages\AMDock\input_tab.py", line 1092, in prepare_receptor
AMDOCK:
AMDOCK: self.target_info = PDBINFO(self.AMDock.target.input)
AMDOCK: File "C:\Users\alexa\Downloads\AMDock-win-master\AMDock-win-master\lib\site-packages\AMDock\tools.py", line 191, in init
AMDOCK:
AMDOCK: self.center = self.mol.getCenter()
AMDOCK: File "C:\Users\alexa\Downloads\AMDock-win-master\AMDock-win-master\lib\site-packages\MolKit\molecule.py", line 1578, in getCenter
AMDOCK:
AMDOCK: self.center = sum(coords)/(len(coords)*1.0)
AMDOCK: File "C:\Users\alexa\Downloads\AMDock-win-master\AMDock-win-master\lib\site-packages\numpy\oldnumeric\functions.py", line 22, in sum
AMDOCK:
AMDOCK: return np.sum(x, axis)
AMDOCK: File "C:\Users\alexa\Downloads\AMDock-win-master\AMDock-win-master\lib\site-packages\numpy\core\fromnumeric.py", line 2076, in sum
AMDOCK:
AMDOCK: initial=initial)
AMDOCK: File "C:\Users\alexa\Downloads\AMDock-win-master\AMDock-win-master\lib\site-packages\numpy\core\fromnumeric.py", line 84, in _wrapreduction
AMDOCK:
AMDOCK: return reduction(axis=axis, out=out, **passkwargs)
AMDOCK: TypeError
AMDOCK: :
AMDOCK: 'ChainSet' object is not callable
AMDOCK: