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(Linux and macOS) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina

License: GNU General Public License v3.0

Python 99.73% CSS 0.27%

amdock docking autodock autodock4zn vina pymol scoring

amdock's Introduction

AMDock: Assisted Molecular Docking with Autodock4 and Autodock Vina

AMDock (Assisted Molecular Docking) is a user-friendly graphical tool to assist in the docking of protein-ligand complexes using Autodock-Vina or AutoDock4. This tool integrates several external programs for processing docking input files, define the search space (box) and perform docking under user’s supervision.

Version 1.6.x for Linux (Build 1.6.1-beta)

DOCUMENTATION

Manual, tutorials and test files are located in Doc folder. (May be out of date. Please check the wiki)

Cite us

Valdes-Tresanco, M.S., Valdes-Tresanco, M.E., Valiente, P.A. and Moreno E. AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4. Biol Direct 15, 12 (2020). https://doi.org/10.1186/s13062-020-00267-2

INSTALL

Installation can be carried out in two ways

(For Linux only) Using a conda environment.

Note: macOS users can use this procedure, however, PyMOL must be compiled using this environment's Python interpreter, since there is no working version of PyMOL for mac in the anaconda repositories.

To do this, proceed as follows:

If you don't have conda installed, please visit the Miniconda download page.

Those with an existing conda installation may wish to create a new conda "environment" to avoid conflicts with what you already have installed. To do this:

conda create --name AMDock python=3.9
conda activate AMDock

(Note that you would need to perform the "conda activate" step every time you wish to use AMDock in a new terminal; it might be appropriate to add this to your start-up script. Creating a new environment should not be necessary if you only use conda for AMDock.)

Once this is done, type:

conda install -c conda-forge pymol-open-source openbabel pdb2pqr

and finally:

python -m pip install git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3 PyQt5
python -m pip install AMDock

Using the OS Python 3 environment. To do this, proceed as follows:

sudo apt install pymol openbabel

(Note that this version of AMDock works with openbabel 3.x)

python3 -m pip install pdb2pqr PyQt5
python3 -m pip install git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3
python3 -m pip install AMDock

Before using AMDock, you most install the PyMOL plugin (grid_amdock.py).

If it does not appear please follow the instructions:

Download the grid_amdock.py file
Open PyMOL > Plugins > Manager Plugins > Install New Plugin > Choose File and select the grid_amdock.py file
Restart PyMOL

To open AMDock, type in the terminal:

AMDock

Note: You can add this line to the .bashrc file to activate de AMDock conda environment and execute AMDock directly

alias amdock="conda activate AMDock; AMDock"

For macOS users,

To view the update history, please check Changes_History file

TUTORIALS

Please, check the wiki https://github.com/Valdes-Tresanco-MS/AMDock-win/wiki

Support

This project is possible thanks to the Open Source license of the JetBrains programs.

amdock's People

Contributors

Stargazers

Watchers

Forkers

minghao2016 ramstein unixjunkie giribio truatpasteurdotfr echukwuka prasadtk amdens-sci dualword feigeliudan01 rnaimehaom stevenabing hasihays melarok arunkantholi

amdock's Issues

please add M1 apple support

Unable to install

I am using linuxmint and used pip to install but following errors are coming. How ever pymol is installed

AMDock
Traceback (most recent call last):
File "/home/nayan/miniconda3/bin/AMDock", line 5, in
from AMDock.Docking_Program import run
File "/home/nayan/miniconda3/lib/python3.9/site-packages/AMDock/Docking_Program.py", line 9, in
from AMDock.result_tab import Results
File "/home/nayan/miniconda3/lib/python3.9/site-packages/AMDock/result_tab.py", line 9, in
from AMDock.variables import Variables
File "/home/nayan/miniconda3/lib/python3.9/site-packages/AMDock/variables.py", line 6, in
import AutoDockTools, pymol
ModuleNotFoundError: No module named 'pymol'

Could not use the docked output on WebGro for Dynamics

We tried uploading the docked complex in pdb format on to WebGro ([https://simlab.uams.edu/]. But, it keeps throwing "protein preprocessing error".

Any help is appreciated.

Fail to install on Ubuntu 22.04 using the OS Python 3 environment

dell@dell-OptiPlex-Tower-Plus-7010:~/Desktop$ python3 -m pip install git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3
Defaulting to user installation because normal site-packages is not writeable
Collecting git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3
Cloning https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3 to /tmp/pip-req-build-pw6k2rbv
Running command git clone --filter=blob:none --quiet https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3 /tmp/pip-req-build-pw6k2rbv
fatal: unable to access 'https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3/': Failed to connect to github.com port 443 after 130074 ms: Connection timed out
error: subprocess-exited-with-error

× git clone --filter=blob:none --quiet https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3 /tmp/pip-req-build-pw6k2rbv did not run successfully.
│ exit code: 128
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× git clone --filter=blob:none --quiet https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3 /tmp/pip-req-build-pw6k2rbv did not run successfully.
│ exit code: 128
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

Unable to start AMDock

I installed AMDock withing a conda environment, as instructed. When I try to launch AMDock, I get the followin errors:

Qt: Session management error: None of the authentication protocols specified are supported
Traceback (most recent call last):
  File "/home/martel/miniconda3/envs/AMDock/bin/AMDock", line 8, in <module>
    sys.exit(run())
  File "/home/martel/miniconda3/envs/AMDock/lib/python3.10/site-packages/AMDock/Docking_Program.py", line 160, in run
    splash = SplashScreen(QPixmap(v.splashscreen_path), app)
  File "/home/martel/miniconda3/envs/AMDock/lib/python3.10/site-packages/AMDock/splash_screen.py", line 37, in __init__
    progress_bar.setValue(ml)
TypeError: setValue(self, int): argument 1 has unexpected type 'float'

I am running Ubuntu 18.04 and Miniconda 4.8.2 with Python 3.10.6 . The PyMOL installation within the AMDock environment works
fine.

I tried fixing the error by using the 'int' function on the argument of setValue, but then the sa,e error crops up on the followinng functions:

self.nposes_value.setMinimum(1.0)
self.nposes_value.setMaximum(20.0)
self.nposes_value.setSingleStep(1.0)

when I replace those arguments with integers values the program loads to the main panel, but when I click
on any of the buttons to select a docking program, I get a crash with thte following errors:

Qt: Session management error: None of the authentication protocols specified are supported

Unhandled Python exception
Aborted (core dumped)

Thanks,
Paulo

Unable to execute

After installation, during execution received following error

(base) debanjan@debanjan:~/AM-Dock/AMDock$ bash AMDock.sh
Traceback (most recent call last):
File "/home/debanjan/AM-Dock/AMDock/AMDock/Docking_Program.py", line 3, in
from checker import Checker
File "/home/debanjan/AM-Dock/AMDock/AMDock/checker.py", line 1, in
from warning import (prot_with_metal_warning, metal_no_ADzn_warning1,
File "/home/debanjan/AM-Dock/AMDock/AMDock/warning.py", line 1, in
from PyQt4 import QtGui
ModuleNotFoundError: No module named 'PyQt4'

Error from external program

If an external program does not terminate correctly, the program may exhibit inconsistencies

Using PyMOL installed with macport on macOS 10.13.6?

Hi,
Is it possible to use AMDock with PyMOL installed with macport on macOS 10.13.6? In this case pathway of PyMOL starting script is /opt/local/bin/pymol.
I've tried to compile pymol directly from source but it failed...
Laurent

Stop docking process

If the docking process is stopped, the program may show inconsistencies

error in Running Prepare_Receptor4...

AMDOCK: Running Prepare_Receptor4 for Target...

set verbose to True
set cleanup to nphs_lps_waters_nonstdres_deleteAltB
Traceback (most recent call last):
File "/media/mario/92bb1dc0-1f5c-4566-bfea-709a64de54f8/mario/Programs/Installation/AmberTools20/amber20/miniconda/envs/AMDock/lib/python3.9/site-packages/AutoDockTools/Utilities24/prepare_receptor4.py", line 157, in
mols = Read(receptor_filename)
File "/media/mario/92bb1dc0-1f5c-4566-bfea-709a64de54f8/mario/Programs/Installation/AmberTools20/amber20/miniconda/envs/AMDock/lib/python3.9/site-packages/MolKit/init.py", line 38, in Read
raise AssertionError("%s does't exist" % filename)
AssertionError: complex_min_h.pdb does't exist

change protein format in visualization

change structure of protein in pdbqt format by pdb format in visualization of all poses of ligand

Docking ligands with exotic metals

I have furnished the AMDock (linux) program with a modified dat file that contains parameters for Ruthenium (Ru) as follows:

atom_par Ru 4.04 0.010 34.5257 -0.00110 0.0 0.0 2 -1 -1 4 # Non H-bonding Ruthenium
atom_par RU 4.04 0.010 34.5257 -0.00110 0.0 0.0 2 -1 -1 4 # Non H-bonding Ruthenium

Furnishing the above parameters was sufficient to enable the docking to proceed. However, there was a warning message as follows:

"Unable to assign MAP type to atom Ru
Sorry, there are no Gasteiger parameters available for atom HB1_yas:B:HB11307:RU1
Unable to assign XYZ type to atom Ru
Unable to assign HYB type to atom Ru"

QUESTION: I am not sure how much it might matter to be able to provide Gasteiger parameters for Ruthenium, but would this be possible to do? What would I need to do to supply this additional information to the program? For example, if I were to use a quantum chemistry program such as Gaussian to determine partial atomic charges (e.g., Mulliken or Lowdin if not Gasteiger), could these be used? If so, how would I provide these charges to the docking program? Instead of partial atomic charges, would it be possible to use integer formal charges? For example, in my ligand, the oxidation state of Ru is Ru2+.

Which file formats can be used as input to AMDock for the receptor and the ligand? (e.g., pdb, sdf, mol2, xyz, etc.)
Can AMDock be used for virtual screening (e.g., of a multi-ligand sdf file) or inverse docking (one or a few ligands docked into an ensemble of receptors)?
Would it be possible for you to integrate Autodock-GPU into your AMDock program?
There might be a small bug in your software. The PDB files in the output could not be read by my main molecular viewer, YASARA-Structure. The ATOM/HETATM data has been placed in the wrong column starting with line 4. I was able to view the file after moving the column by one space.

Thank you for creating a program that is much easier to use than Autodock Tools!

-- RJR

unable to install

i tried to install AMDock using the given method but getting following errors

(base) shrikant@shrikant-HP:~$ amdock
Traceback (most recent call last):
File "/home/shrikant/miniconda3/envs/AMDock/bin/AMDock", line 5, in
from AMDock.Docking_Program import run
File "/home/shrikant/miniconda3/envs/AMDock/lib/python3.9/site-packages/AMDock/Docking_Program.py", line 9, in
from AMDock.result_tab import Results
File "/home/shrikant/miniconda3/envs/AMDock/lib/python3.9/site-packages/AMDock/result_tab.py", line 9, in
from AMDock.variables import Variables
File "/home/shrikant/miniconda3/envs/AMDock/lib/python3.9/site-packages/AMDock/variables.py", line 6, in
import AutoDockTools, pymol
File "/home/shrikant/miniconda3/envs/AMDock/lib/python3.9/site-packages/pymol/init.py", line 558, in
import pymol._cmd
ImportError: /home/shrikant/miniconda3/envs/AMDock/lib/python3.9/site-packages/pymol/../../../libnetcdf.so.19: undefined symbol: H5Pset_fapl_ros3

Feature Request

Hey,
AMDock is extremely useful and I personally know a lot of people liking it. However, it would be great if you could include flexible docking and virtual screening into AMDock.

I have to talk on this repository soon.

Will you reply here something. or contact me at +16268031601 or [email protected]

version `GLIBCXX_3.4.26' not found

AMDock
Traceback (most recent call last):
File "/media/mario/92bb1dc0-1f5c-4566-bfea-709a64de54f8/mario/Programs/Installation/AmberTools20/amber20/miniconda/envs/AMDock/bin/AMDock", line 7, in
from AMDock.Docking_Program import run
File "/media/mario/92bb1dc0-1f5c-4566-bfea-709a64de54f8/mario/Programs/Installation/AmberTools20/amber20/miniconda/envs/AMDock/lib/python3.9/site-packages/AMDock/Docking_Program.py", line 9, in
from AMDock.result_tab import Results
File "/media/mario/92bb1dc0-1f5c-4566-bfea-709a64de54f8/mario/Programs/Installation/AmberTools20/amber20/miniconda/envs/AMDock/lib/python3.9/site-packages/AMDock/result_tab.py", line 9, in
from AMDock.variables import Variables
File "/media/mario/92bb1dc0-1f5c-4566-bfea-709a64de54f8/mario/Programs/Installation/AmberTools20/amber20/miniconda/envs/AMDock/lib/python3.9/site-packages/AMDock/variables.py", line 6, in
import AutoDockTools, pymol
File "/media/mario/92bb1dc0-1f5c-4566-bfea-709a64de54f8/mario/Programs/Installation/AmberTools20/amber20/miniconda/envs/AMDock/lib/python3.9/site-packages/pymol/init.py", line 558, in
import pymol._cmd
ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /media/mario/92bb1dc0-1f5c-4566-bfea-709a64de54f8/mario/Programs/Installation/AmberTools20/amber20/miniconda/envs/AMDock/lib/python3.9/site-packages/pymol/_cmd.cpython-39-x86_64-linux-gnu.so)

don't use sudo with your script without warning

Please, as a courtesy to your users, do not hide the sudo commands in your install.sh script.

If needed ask them to re-run ./install.sh with sudo.

Problems running the shell script on ubuntu 20.04

Unfortunately it is not possible to install pyqt4 without compiling it from scratch (it is no longer supported in the python repository or even in the official ubuntu, or debian repos) but I cant compile it even after installing the sip required package. It is a shame that the windows version works so well. Cant you just give us a compiled software like the windows version has?

is python2.7 required ?

hi again,

AMDock/AMDock.sh contains:

PYMOL_PATH=${PYMOL_PATH:=`python2.7 -c "from imp import find_module; print find_module('pymol')[1]"`}

Is the python2.7 version for pymol required? or only the python used to build pymol is needed here?

I have also replaced the PYMOL_* with:

PYMOL_DATA=${PYMOL_PATH}/pymol_path/data
PYMOL_SCRIPTS=${PYMOL_PATH}/pymol_path/scripts
CHEMPY_DATA=${PYMOL_PATH}/pymol_path/data/chempy

as we don't have pymol installed in /usr

many versions of pymol not working

what is current version of pymol confirmed to work with which python? I had successfully set up a version of pymol that worked with linux focal fossa, my python was autoupdated, and now I cannot get it to work, AMD dock will run still, but the open in pymol opens pymol 2.5 and does not load results

'Segmentation fault: 11' error when quit AMDock on macOS 12

Running AMDock successfully on macOS 12 , however when quit the app, it would report 'Segmentation fault: 11' error. I don't know how to debug it. Here is the error report details.

Thanks.

Protein ligand docking using AMDock was unsuccessful

Hi,
Today I tried to perform protein-ligand docking using the autodock-vina module of AMDock. I had prior knowledge about the ligand-binding site and hence I selected the "center on residues" option in the "define search space" section and went ahead with it. However, this step was not successful and I got an error. It was written as "ValueError: invalid literal for float(): -1.#QO". Being unaware of coding languages I don't understand what does it mean. I would request anyone who understands this issue to kindly help me to solve it.
Thank You
sacyp_csa_dock_proj1.log

New version unable to execute

install grid_amdock.py with in Pymol plugin still bellow error persists

Traceback (most recent call last):
File "/home/debanjan/amber20/miniconda/bin/AMDock", line 5, in
from AMDock.Docking_Program import run
File "/home/debanjan/amber20/miniconda/lib/python3.9/site-packages/AMDock/Docking_Program.py", line 9, in
from AMDock.result_tab import Results
File "/home/debanjan/amber20/miniconda/lib/python3.9/site-packages/AMDock/result_tab.py", line 9, in
from AMDock.variables import Variables
File "/home/debanjan/amber20/miniconda/lib/python3.9/site-packages/AMDock/variables.py", line 6, in
import AutoDockTools, pymol
ModuleNotFoundError: No module named 'pymol'

TypeError: setValue(self, value: int): argument 1 has unexpected type 'float'

After sucessful installation of the program using protocol provided, I receive the following error:

#$ AMDock
Traceback (most recent call last):
  File "/home/anaconda3/envs/AMDock/bin/AMDock", line 8, in <module>
    sys.exit(run())
             ^^^^^
  File "/home/anaconda3/envs/AMDock/lib/python3.11/site-packages/AMDock/Docking_Program.py", line 160, in run
    splash = SplashScreen(QPixmap(v.splashscreen_path), app)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anaconda3/envs/AMDock/lib/python3.11/site-packages/AMDock/splash_screen.py", line 37, in __init__
    progress_bar.setValue(ml)
TypeError: setValue(self, value: int): argument 1 has unexpected type 'float'

Do you think this can be fixed by converting the float value to an integer?

progress_bar.setValue(int(ml))

A second option but long-winded one I see is using different Splash widget altogether.

AMDock macOS 10.13.6 issue

After successful installation of AMDock I tried to run a re docking on AutoDock Vina but after setting Project (Project Progress 25.0%) and loading Target and Ligand with Prepare Input successfully I wasn't able to select Target option in Search Space area with an alert window "The working directory was not found or it does not have permission for writing. Please reset the program."

Welcome to AMDock
Version 1.6.2 For Windows and Linux

Test log
AMDOCK: Defining Initial Parameters...
AMDOCK: DOCKING_PROGRAM: AutoDock Vina
AMDOCK: WDIR: /Users/xxxx/Downloads/Test
AMDOCK: MODE: SIMPLE
AMDOCK: TARGET: 6fvf
AMDOCK: TARGET (Hetero): [['A', '503401'], ['A', 'ATP402']]
AMDOCK: TARGET (Zn atoms): []
AMDOCK: LIGAND: aza_ester
AMDOCK: LIGAND (heavy_atoms): 32
AMDOCK: Defining Initial Parameters... Done
AMDOCK: Prepare Initial Files...

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