ccsb-scripps / autodock-vina Goto Github PK

permissions denied with macos executable: ./vina_1.2.0_macos_x86_64 --help
source not found using miniconda: conda install -c conda-forge -c ccsb-scripps vina

your help with macOS installation would be greatly appreciated

I realized that the example input data for the receptor have the suffix "H", I believe that means the hydrogen atoms have been added. However, I found a hard time reproducing the input file provided. More specifically, I found that the receptor files (both pdb and pdbqt), taking the basic docking as an example, start with serine residue before the methionine. I wonder whether that will make a difference for the subsequent docking. consequently, I used the "reduce" as suggested in the tutorial to add the hydrogen atoms, but my output seems does not match the file provided in the tutorial.

I just want to make sure I have all my steps right so that I can translate these codes for docking my receptor and ligand pairs.

Thanks!

I'm following the great tutorial you guys made for vina recently. I have two questions hope that you can point me in the right direction, or make the contact with someone that could help me out:

1. On step 3 of the tutorial, needs a script called prepare_gpf.py in the <autodock-vina_directory>/example/autodock_scripts directory. Could you point me to how to download that directory? As a note, I downloaded vina from the github. I also checked on the supplementary data of the Nature protocols paper, but it seems that is not the right place to look for.

2. More generally: do you recommend reference to learn how to get a grid box for docking? And, if I understand correctly, using autodock4 forcefield to compute the affinity map helps bypass the need to specify the grid box, correct? Would you recommend using ad4 instead of specifying the box?

Thank you and kudos to your work !

I downloaded the 1.2.2 release binary to Ubuntu 20.04, and it crashed very quickly after I launched the program with the message "killed", while I set verbosity=2, I still didn't see much command output.

Center: X 209.65 Y 192.37 Z 296.58
Size: X 10 Y 18 Z 24
Grid space: 0.375
Exhaustiveness: 8
CPU: 12
Verbosity: 2

Killed

When I used the 1.1.2 (the windows version), the same command runs fine for 4 hours. (~50%), I have hoped to the 1.2.2 version would allow us get results faster.

When I do mk_prepare_ligand.py -i 1uw6_ligand.sdf -o 1uw6_ligand.pdbqt --pH 7.4 -w
I get -> RuntimeError: Cannot place water molecules on atom 7 of type NA with 4 neighbors.
It's error in code and if to add this key 4: (1, 3) in self._hb_config for key 'NA', it also have some problems (adding one extra water, for example: 5 water for protonated ammonia where 2 molecules of water have equal coordinates). For nicotine it's the same.
If it's possible, please check and fix it. Thanks!

Hi,

I have issues with "prepare_receptor".
When I read 1iep.pdb in the audock vina document, it worked fine.

But, In5tgz.pdb, It worked with the following warning message.
"""
WARNING! 5tgz has 16 atoms with alternate locations named ['A', 'B']!

WARNING! using alternate location A
"""

Also, when I read 5e8m.pdb, 1p0i.pdb, 5e97.pdb, 5e98.pdb, and etc, it failed with the following error message.
ex) About 1p0i.pdb
"""
WARNING! 1p0i has 66 atoms with alternate locations named ['A', 'B']!

WARNING! using alternate location A
'B ' apparently composed of not std residues. Deleting
'C ' apparently composed of not std residues. Deleting

AttributeError: member babel_type not found
"""

Why the error occurs and how to fix it?

Best,
kyudam

How can I correctly use '--local_only' to get the score, as in '--score_only'?I have tested that '-- score_only 'does not score as '-- score_only'.

When doing the tutorial everything works until I try to run Vina. Every time I try to run Vina I get zsh: permission denied: ./vina_1.2.2_macos_x86_64. Is there something I did wrong with the installation?

Hello,
I'm a bit new to AutoDock-Vina and all this in-silco screen process so if my questions are stupid.
I'm trying to calculate the energy of docking a molecule to a protein,
I tried using the 1iep receptor and 1iep ligand that was given in the python example.

after that, I tried using a different molecule of my choosing that has the following SMILES string: C[C@@]1(c2cc(NC(=O)c3ccc(C#N)cn3)ccc2F)CSCC(N)=N1

I converted the molecule from smi file to pdb using obabel and the following command
obabel -i smi ./mol.smi -O ./mol.pdb --gen3d

after that I used the mk_prepare_ligand on that file to create the pdbqt file using the following command
python3 mk_prepare_ligand.py -i ./mol.pdb -o ./mol.pdbqt

then I tried running the python example again but with my molecule and I got the following error:

>>> from vina import Vina
>>> v = Vina(sf_name='vina')
>>> v.set_receptor('./1iep_receptor.pdbqt')
>>> v.set_ligand_from_file('./mol.pdbqt')
>>> v.compute_vina_maps(center=[15.190, 53.903, 16.917], box_size=[20, 20, 20])
Computing Vina grid ... done.
>>> energy = v.score()
ERROR: The ligand is outside the grid box. Increase the size of the grid box or center it accordingly around the ligand.

I tried looking it up, but I couldn't find any solution
so my questions are the following:

1. what does exactly vina_maps mean, is it the location on the protein/receptor itself the docking occurs?
2. is the vina_map depend on the protein/receptor itself or on both protein/receptor and the ligand/molecule?
3. if I want to use a different protein/receptor in future experiments, how exactly do I compute those vina maps?
4. did I convert the molecule to ligand pdbqt file correctly?
5. where I can learn more about molecular docking

thank you and sorry if my question are bad

I'm Mac M1, Monterey 12.0.1 user

I try to install auto dock vina using Conda environment refer to installation guide

$ conda create -n vina python=3
$ conda activate vina
$ conda config --env --add channels conda-forge

$ conda install numpy
$ pip install vina

but I thin install vina was fail and I could only see the this massage

I'm so glad If you let me know how I can solve it

While vina python library gets easily installed on linux and on WSL, facing issues installing it for Windows.

error.log

Prior to pip install vina command, installed boost, boost-cpp, py-boost and swig as well. Error still persists saying

Boost library is not installed in this conda environment
and ERROR: No matching distribution found for vina

(Env was created with both python 3.7 and 3.8)

Complete error is attached

I believe this to be a bug with Vina 1.2

Environment Information

Vina: 1.2.3

OS: Centos 7.6

Data set: https://github.com/gkxiao/very-negative-vina-score

Expected Behavior

pose_1.pdbqt is a docking pose from a command line calculation, the expected affinity score is -7.925 as following:

from vina import Vina
#create docking object
receptor = 'receptor.pdbqt'
ligand = 'pose_1.pdbqt'
output = 'pose_1_out.pdbqt'
dock = Vina(sf_name='vina',seed=-1280817548,verbosity=2)
dock.set_receptor(receptor)
center =  [5.061, 2.751, 17.703]
box_size = [15, 15, 15]
dock.compute_vina_maps(center=center, box_size=box_size)
dock.set_ligand_from_file(ligand)
#dock.dock()
energy = dock.score()
print('Score before minimization: %.3f (kcal/mol)' % energy[0])

Score before minimization: -7.925 (kcal/mol)

Vina Binary version gives the same results.

vina_1.2 --config docking.conf --ligand pose_1.pdbqt --score_only --verbosity 2

#################################################################
# If you used AutoDock Vina in your work, please cite:          #
#                                                               #
# O. Trott, A. J. Olson,                                        #
# AutoDock Vina: improving the speed and accuracy of docking    #
# with a new scoring function, efficient optimization and       #
# multithreading, Journal of Computational Chemistry 31 (2010)  #
# 455-461                                                       #
#                                                               #
# DOI 10.1002/jcc.21334                                         #
#                                                               #
# Please see http://vina.scripps.edu for more information.      #
#################################################################
Scoring function : vina
Rigid receptor: receptor.pdbqt
Ligand: pose_1.pdbqt
Center: X 5.061 Y 2.751 Z 17.703
Size: X 15 Y 15 Z 15
Grid space: 0.375
Exhaustiveness: 8
CPU: 0
Verbosity: 2
Computing Vina grid ... done.
Estimated Free Energy of Binding   : -7.925 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : -10.241 (kcal/mol)
Ligand - Receptor              : -10.241 (kcal/mol)
Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : -0.693 (kcal/mol)
Ligand                         : -0.693 (kcal/mol)
Flex   - Receptor              : 0.000 (kcal/mol)
Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : 2.316 (kcal/mol)
(4) Unbound System's Energy        : -0.693 (kcal/mol)

Actual Behavior

Howerver, the python script in cammond line gives total differnt results: -149kcal/mol:

python docking.py

Computing Vina grid ... done.
WARNING: At low exhaustiveness, it may be impossible to utilize all CPUs.
Performing docking (random seed: -1280817548) ... 
0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
done.
ENERGY FROM SEARCH: -10.9406
FINAL ENERGY: 
Estimated Free Energy of Binding   : -149.841 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : -10.251 (kcal/mol)
    Ligand - Receptor              : -10.251 (kcal/mol)
    Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : -0.689 (kcal/mol)
    Ligand                         : -0.689 (kcal/mol)
    Flex   - Receptor              : 0.000 (kcal/mol)
    Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : 43.799 (kcal/mol)
(4) Unbound System's Energy        : 182.700 (kcal/mol)
ENERGY FROM SEARCH: -10.619
FINAL ENERGY: 
Estimated Free Energy of Binding   : -149.589 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : -10.422 (kcal/mol)
    Ligand - Receptor              : -10.422 (kcal/mol)
    Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : -0.192 (kcal/mol)
    Ligand                         : -0.192 (kcal/mol)
    Flex   - Receptor              : 0.000 (kcal/mol)
    Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : 43.725 (kcal/mol)
(4) Unbound System's Energy        : 182.700 (kcal/mol)
ENERGY FROM SEARCH: -9.823
FINAL ENERGY: 
Estimated Free Energy of Binding   : -148.981 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : -8.748 (kcal/mol)
    Ligand - Receptor              : -8.748 (kcal/mol)
    Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : -1.080 (kcal/mol)
    Ligand                         : -1.080 (kcal/mol)
    Flex   - Receptor              : 0.000 (kcal/mol)
    Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : 43.547 (kcal/mol)
(4) Unbound System's Energy        : 182.700 (kcal/mol)
ENERGY FROM SEARCH: -9.808
FINAL ENERGY: 
Estimated Free Energy of Binding   : -148.968 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : -9.376 (kcal/mol)
    Ligand - Receptor              : -9.376 (kcal/mol)
    Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : -0.435 (kcal/mol)
    Ligand                         : -0.435 (kcal/mol)
    Flex   - Receptor              : 0.000 (kcal/mol)
    Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : 43.543 (kcal/mol)
(4) Unbound System's Energy        : 182.700 (kcal/mol)
ENERGY FROM SEARCH: -9.693
FINAL ENERGY: 
Estimated Free Energy of Binding   : -148.878 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : -8.934 (kcal/mol)
    Ligand - Receptor              : -8.934 (kcal/mol)
    Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : -0.762 (kcal/mol)
    Ligand                         : -0.762 (kcal/mol)
    Flex   - Receptor              : 0.000 (kcal/mol)
    Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : 43.517 (kcal/mol)
(4) Unbound System's Energy        : 182.700 (kcal/mol)
ENERGY FROM SEARCH: -9.053
FINAL ENERGY: 
Estimated Free Energy of Binding   : -148.377 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : -8.214 (kcal/mol)
    Ligand - Receptor              : -8.214 (kcal/mol)
    Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : -0.834 (kcal/mol)
    Ligand                         : -0.834 (kcal/mol)
    Flex   - Receptor              : 0.000 (kcal/mol)
    Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : 43.371 (kcal/mol)
(4) Unbound System's Energy        : 182.700 (kcal/mol)
ENERGY FROM SEARCH: -9.180
FINAL ENERGY: 
Estimated Free Energy of Binding   : -148.483 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : -9.501 (kcal/mol)
    Ligand - Receptor              : -9.501 (kcal/mol)
    Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : 0.316 (kcal/mol)
    Ligand                         : 0.316 (kcal/mol)
    Flex   - Receptor              : 0.000 (kcal/mol)
    Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : 43.402 (kcal/mol)
(4) Unbound System's Energy        : 182.700 (kcal/mol)
ENERGY FROM SEARCH: -8.835
FINAL ENERGY: 
Estimated Free Energy of Binding   : -148.213 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : -8.022 (kcal/mol)
    Ligand - Receptor              : -8.022 (kcal/mol)
    Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : -0.813 (kcal/mol)
    Ligand                         : -0.813 (kcal/mol)
    Flex   - Receptor              : 0.000 (kcal/mol)
    Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : 43.323 (kcal/mol)
(4) Unbound System's Energy        : 182.700 (kcal/mol)
ENERGY FROM SEARCH: -8.624
FINAL ENERGY: 
Estimated Free Energy of Binding   : -148.057 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : -8.141 (kcal/mol)
    Ligand - Receptor              : -8.141 (kcal/mol)
    Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : -0.493 (kcal/mol)
    Ligand                         : -0.493 (kcal/mol)
    Flex   - Receptor              : 0.000 (kcal/mol)
    Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : 43.277 (kcal/mol)
(4) Unbound System's Energy        : 182.700 (kcal/mol)
ENERGY FROM SEARCH: -8.157
FINAL ENERGY: 
Estimated Free Energy of Binding   : -147.690 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : -7.094 (kcal/mol)
    Ligand - Receptor              : -7.094 (kcal/mol)
    Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : -1.066 (kcal/mol)
    Ligand                         : -1.066 (kcal/mol)
    Flex   - Receptor              : 0.000 (kcal/mol)
    Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : 43.170 (kcal/mol)
(4) Unbound System's Energy        : 182.700 (kcal/mol)
ENERGY FROM SEARCH: -8.324
FINAL ENERGY: 
Estimated Free Energy of Binding   : -138.088 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : 4.966 (kcal/mol)
    Ligand - Receptor              : 4.966 (kcal/mol)
    Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : -0.718 (kcal/mol)
    Ligand                         : -0.718 (kcal/mol)
    Flex   - Receptor              : 0.000 (kcal/mol)
    Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : 40.363 (kcal/mol)
(4) Unbound System's Energy        : 182.700 (kcal/mol)
ENERGY FROM SEARCH: -8.091
FINAL ENERGY: 
Estimated Free Energy of Binding   : -141.540 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : 0.372 (kcal/mol)
    Ligand - Receptor              : 0.372 (kcal/mol)
    Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : -0.584 (kcal/mol)
    Ligand                         : -0.584 (kcal/mol)
    Flex   - Receptor              : 0.000 (kcal/mol)
    Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : 41.372 (kcal/mol)
(4) Unbound System's Energy        : 182.700 (kcal/mol)
ENERGY FROM SEARCH: -8.126
FINAL ENERGY: 
Estimated Free Energy of Binding   : -147.664 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : -7.620 (kcal/mol)
    Ligand - Receptor              : -7.620 (kcal/mol)
    Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : -0.507 (kcal/mol)
    Ligand                         : -0.507 (kcal/mol)
    Flex   - Receptor              : 0.000 (kcal/mol)
    Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : 43.162 (kcal/mol)
(4) Unbound System's Energy        : 182.700 (kcal/mol)
ENERGY FROM SEARCH: -6.997
FINAL ENERGY: 
Estimated Free Energy of Binding   : -146.795 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : -8.043 (kcal/mol)
    Ligand - Receptor              : -8.043 (kcal/mol)
    Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : 1.040 (kcal/mol)
    Ligand                         : 1.040 (kcal/mol)
    Flex   - Receptor              : 0.000 (kcal/mol)
    Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : 42.908 (kcal/mol)
(4) Unbound System's Energy        : 182.700 (kcal/mol)
ENERGY FROM SEARCH: -5.683
FINAL ENERGY: 
Estimated Free Energy of Binding   : -145.777 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : -4.769 (kcal/mol)
    Ligand - Receptor              : -4.769 (kcal/mol)
    Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : -0.919 (kcal/mol)
    Ligand                         : -0.919 (kcal/mol)
    Flex   - Receptor              : 0.000 (kcal/mol)
    Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : 42.611 (kcal/mol)
(4) Unbound System's Energy        : 182.700 (kcal/mol)
ENERGY FROM SEARCH: -5.912
FINAL ENERGY: 
Estimated Free Energy of Binding   : -135.714 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : 7.984 (kcal/mol)
    Ligand - Receptor              : 7.984 (kcal/mol)
    Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : -0.667 (kcal/mol)
    Ligand                         : -0.667 (kcal/mol)
    Flex   - Receptor              : 0.000 (kcal/mol)
    Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : 39.669 (kcal/mol)
(4) Unbound System's Energy        : 182.700 (kcal/mol)
ENERGY FROM SEARCH: -5.692
FINAL ENERGY: 
Estimated Free Energy of Binding   : -143.846 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : -4.257 (kcal/mol)
    Ligand - Receptor              : -4.257 (kcal/mol)
    Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : 1.065 (kcal/mol)
    Ligand                         : 1.065 (kcal/mol)
    Flex   - Receptor              : 0.000 (kcal/mol)
    Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : 42.046 (kcal/mol)
(4) Unbound System's Energy        : 182.700 (kcal/mol)
ENERGY FROM SEARCH: -5.537
FINAL ENERGY: 
Estimated Free Energy of Binding   : -145.661 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : -4.676 (kcal/mol)
    Ligand - Receptor              : -4.676 (kcal/mol)
    Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : -0.863 (kcal/mol)
    Ligand                         : -0.863 (kcal/mol)
    Flex   - Receptor              : 0.000 (kcal/mol)
    Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : 42.577 (kcal/mol)
(4) Unbound System's Energy        : 182.700 (kcal/mol)
ENERGY FROM SEARCH: -5.444
FINAL ENERGY: 
Estimated Free Energy of Binding   : -141.908 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : 0.098 (kcal/mol)
    Ligand - Receptor              : 0.098 (kcal/mol)
    Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : -0.785 (kcal/mol)
    Ligand                         : -0.785 (kcal/mol)
    Flex   - Receptor              : 0.000 (kcal/mol)
    Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : 41.480 (kcal/mol)
(4) Unbound System's Energy        : 182.700 (kcal/mol)
ENERGY FROM SEARCH: 247.478
FINAL ENERGY: 
Estimated Free Energy of Binding   : 50.180 (kcal/mol) [=(1)+(2)+(3)+(4)]
(1) Final Intermolecular Energy    : 64.848 (kcal/mol)
    Ligand - Receptor              : 64.848 (kcal/mol)
    Ligand - Flex side chains      : 0.000 (kcal/mol)
(2) Final Total Internal Energy    : 182.700 (kcal/mol)
    Ligand                         : 182.700 (kcal/mol)
    Flex   - Receptor              : 0.000 (kcal/mol)
    Flex   - Flex side chains      : 0.000 (kcal/mol)
(3) Torsional Free Energy          : -14.668 (kcal/mol)
(4) Unbound System's Energy        : 182.700 (kcal/mol)
mode |   affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1    -149.8414     0.0000     0.0000
2    -149.5893     0.7274     2.3684
3    -148.9809     3.2994     6.4348
4    -148.9676     1.8543     3.0350
5    -148.8782     1.8490     2.8579
6    -148.4830     2.4573     3.6517
7    -148.3769     3.8287     7.5138
8    -148.2126     3.8224     7.4557
9    -148.0573     2.2618     3.7545
10    -147.6903     3.6454     6.9867
11    -147.6641     1.5086     2.4942
12    -146.7947     1.8645     2.2871
13    -145.7771     2.9325     6.8320
14    -145.6614     3.3765     7.2577
15    -143.8460     3.3936     4.4782
16    -141.9077     2.0037     3.0612
17    -141.5400     1.9712     3.4042
18    -138.0882     1.6318     2.4177
19    -135.7138     3.4993     7.2856
20      50.1802     6.6452     8.4232

Obviously, Very high term 3 and 4 results in the very negative affinity score. By the way, the actual affinity is (1)+(2)+(3)-(4) instead of (1)+(2)+(3)+(4).

Steps to Reproduce

The materials to reproduce the results can be available from: https://github.com/gkxiao/very-negative-vina-score

Your example for flexibledocking is failed.

(base) liuyujie714@ubuntu:~/Documents/flexible_docking/solution$ ./vina_1.2.1_linux_x86_64  --receptor 1fpu_receptor_rigid.pdbqt --flex 1fpu_receptor_flex.pdbqt \
>        --ligand 1iep_ligand.pdbqt --config 1fpu_receptor_rigid_vina_box.txt \
>        --exhaustiveness 32 --out 1fpu_ligand_flex_vina_out.pdbqt
AutoDock Vina v1.2.1
#################################################################
# If you used AutoDock Vina in your work, please cite:          #
#                                                               #
# J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli  #
# AutoDock Vina 1.2.0: New Docking Methods, Expanded Force      #
# Field, and Python Bindings, J. Chem. Inf. Model. (2021)       #
# DOI 10.1021/acs.jcim.1c00203                                  #
#                                                               #
# O. Trott, A. J. Olson,                                        #
# AutoDock Vina: improving the speed and accuracy of docking    #
# with a new scoring function, efficient optimization and       #
# multithreading, J. Comp. Chem. (2010)                         #
# DOI 10.1002/jcc.21334                                         #
#                                                               #
# Please see https://github.com/ccsb-scripps/AutoDock-Vina for  #
# more information.                                             #
#################################################################

Scoring function : vina
Rigid receptor: 1fpu_receptor_rigid.pdbqt
Flex receptor: 1fpu_receptor_flex.pdbqt
Ligand: 1iep_ligand.pdbqt
Center: X 15.19 Y 53.903 Z 16.917
Size: X 20 Y 20 Z 20
Grid space: 0.375
Exhaustiveness: 32
CPU: 0
Verbosity: 1



An unknown error occurred. 

Please report bugs through the Issue Tracker on GitHub 
(https://github.com/ccsb-scripps/AutoDock-Vina/issues)., so
that this problem can be resolved. The reproducibility of the
error may be vital, so please remember to include the following in
your problem report:
* the EXACT error message,
* your version of the program,
* the type of computer system you are running it on,
* all command line options,
* configuration file (if used),
* ligand file as PDBQT,
* receptor file as PDBQT,
* flexible side chains file as PDBQT (if used),
* output file as PDBQT (if any),
* input (if possible),
* random seed the program used (this is printed when the program starts).

Thank you!

In the latest vina version for python 3.9.7 there seems to be an issue with the v.optimize() function or the v.compute_vina_maps() or something in between. It seems vina is not aligning or moving the ligand into the search box before running the minimisation or scoring steps. Here is more explanation:

From the tutorial, 1iep_ligand.pdbqt is found within the search space of 1iep_receptor.pdbqt by default causing no errors. But using the same ligand (from the zinc15 database) with a different starting coordinate location gives "ERROR: The ligand is outside the grid box". This problem does not seem to be present in vina's python 3.8 version, but it is present in vina's python 3.9 version.

Here is how to replicate the error in python 3.9.7 (link to the zinc.pdbqt file - everything else is from vina's github and tutorial):

Python script:
from vina import Vina
v = Vina(sf_name='vina', seed=-1630626792)
v.set_receptor('1iep_receptor.pdbqt') # also replace with zinc.pdbqt
v.set_ligand_from_file('1iep_ligand.pdbqt')
v.compute_vina_maps(center=[15.190, 53.903, 16.917], box_size=[20, 20, 20])
v.optimize()
v.dock(exhaustiveness=32, n_poses=5)

Operating system:
Linux Mint for python 3.8.5
Linux Ubuntu for python 3.9.7

Running on python 3.8.5:
1iep_receptor.pdbqt
Computing Vina grid ... done.
Number of local optimization steps: 22
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -13.4415 0.0000 0.0000
2 -11.4492 3.0314 12.4120
3 -11.3302 3.8301 12.2556
4 -10.9768 1.6118 13.5530
5 -10.6253 2.4966 12.5517

zinc.pdbqt
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -11.3168 0.0000 0.0000
2 -10.0187 2.4323 13.5227
3 -9.2159 7.9696 12.5398
4 -9.0732 3.7733 8.0975
5 -8.9076 2.6083 12.7736

In python 3.9.7:
1iep_receptor.pdbqt
Computing Vina grid ... done.
Number of local optimization steps: 22
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -13.1556 0.0000 0.0000
2 -12.6289 0.8226 1.1902
3 -11.9645 1.0407 1.5865
4 -11.1891 2.9827 12.4195
5 -11.0036 3.7423 12.2485

zinc.pdbqt
Computing Vina grid ... done.
ERROR: The ligand is outside the grid box. Increase the size of the grid box or center it accordingly around the ligand.

Temporary solution:
Commenting out the v.optimize() line stops the Error from happening and the script continues to the docking step, but then no minimisation is taking place before docking.

Question:

1. Is v.optimize() required for virtual screening?
2. Is there a way to fix the code (if this is a bug)?
3. Is there a way to forcefully or manually re-position the ligand within the search space to overcome this error?
4. If the analysis of the error is incorrect, then how to correctly overcome this error?

An error about array out of bounds will be raised when compiling vina with g++ -DDEBUG.

[jcyang@lab:AutoDock-Vina]$ cd build/linux/debug/
[jcyang@lab:debug]$ cat Makefile 
# BASE=/usr
BASE=$(HOME)/opt/boost175
BOOST_VERSION=1_75
BOOST_INCLUDE = $(BASE)/include
C_PLATFORM=-static -pthread
GPP=/usr/bin/g++
C_OPTIONS= -g -DDEBUG -std=gnu++11
BOOST_LIB_VERSION=

include ../../makefile_common
[jcyang@lab:debug]$ make
/usr/bin/g++ -static -pthread -ansi -Wno-long-long -g -DDEBUG -std=gnu++11 -I /home/jcyang/opt/boost175/include  -I ../../../src/lib -o main.o -c ../../../src/main/main.cpp 
......
/usr/bin/g++ -static -pthread -ansi -Wno-long-long -g -DDEBUG -std=gnu++11 -I /home/jcyang/opt/boost175/include -L/home/jcyang/opt/boost175/lib -L. -o vina_split split.o -l boost_system -l boost_thread -l boost_serialization -l boost_filesystem -l boost_program_options
[jcyang@lab:debug]$ cd ../../../example/basic_docking/solution/
[jcyang@lab:solution]$ ../../../build/linux/debug/vina --receptor 1iep_receptor.pdbqt --ligand 1iep_ligand.pdbqt --config 1iep_receptor_vina_box.txt
#################################################################
# If you used AutoDock Vina in your work, please cite:          #
#                                                               #
# O. Trott, A. J. Olson,                                        #
# AutoDock Vina: improving the speed and accuracy of docking    #
# with a new scoring function, efficient optimization and       #
# multithreading, Journal of Computational Chemistry 31 (2010)  #
# 455-461                                                       #
#                                                               #
# DOI 10.1002/jcc.21334                                         #
#                                                               #
# Please see http://vina.scripps.edu for more information.      #
#################################################################

Output will be 1iep_ligand_out.pdbqt
Scoring function : vina
Rigid receptor: 1iep_receptor.pdbqt
Ligand: 1iep_ligand.pdbqt
Center: X 15.19 Y 53.903 Z 16.917
Size: X 20 Y 20 Z 20
Grid space: 0.375
Exhaustiveness: 8
CPU: 0
Verbosity: 1

vina: ../../../src/lib/atom_constants.h:336: fl xs_radius(sz): Assertion `t < n' failed.
Aborted (core dumped)

when an error raised, t is 32, n is 32, and xs_vdw_radii[t] is 2.

Hello,

Is it possible to optimize the ligand using explicit receptor atoms with the "local_only" command, similar to what happens at the end of global_search?

https://github.com/ccsb-scripps/AutoDock-Vina/blob/develop/src/lib/vina.cpp#L825 seems to only perform optimization using the grid.

Effectively, my use case is to try to split up global_search into 2 parts. First, I generate a list of poses with no_refine = true, skipping this final local optimization. Then, as a second step, I would like to go through those final poses and run local optimization just like at the end of global_search. This way, I can perform multiple runs of Vina, collect all the results together, manually remove redundant ligands, and then perform the final local optimization to get the final pose/score.

Help by the way seems to suggest that local_only should explicitly use receptor atoms if the receptor is present:

--no_refine
when --receptor is provided, do not use
explicit receptor atoms (instead of
precalculated grids) for: (1) local
optimization and scoring after docking,
(2) --local_only jobs, and (3)
--score_only jobs

Thanks,
Chris

Hi,

Is there a way to output docking scores with more sig figs? In the previous version (v1.1.2), we used "--score_only " flag with top docked poses. We tried to use this flag in this new version (v1.2.2) but we couldn't get more sig figs.

I attached our input files and protocol we used.

Thanks!

score_only.zip

Dear AutoDock-vina developers,

Frist: Thank you very much for further improving the docking calculations by this new release. I'm very interested in running vina using the newly implemented python scripting possibilities and therefor tried to set it up (from source). Building the binary was not an issue at all but when it comes to compile the python bindings, I got an compile error:

creating build/lib.linux-x86_64-3.5/vina
x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fdebug-prefix-map=/build/python3.5-ipWR6Y/python3.5-3.5.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
build/temp.linux-x86_64-3.5/src/lib/utils.o:(.bss+0x0): multiple definition of `boost::system::throws'
build/temp.linux-x86_64-3.5/src/lib/random.o:(.bss+0x0): first defined here
build/temp.linux-x86_64-3.5/src/lib/vina.o:(.bss+0x0): multiple definition of `boost::system::throws'
build/temp.linux-x86_64-3.5/src/lib/random.o:/usr/include/boost/system/detail/error_code.ipp:66: first defined here
build/temp.linux-x86_64-3.5/src/lib/quaternion.o:(.bss+0x0): multiple definition of `boost::system::throws'
build/temp.linux-x86_64-3.5/src/lib/random.o:/usr/include/boost/system/detail/error_code.ipp:66: first defined here
build/temp.linux-x86_64-3.5/src/lib/monte_carlo.o:(.bss+0x0): multiple definition of `boost::system::throws'
build/temp.linux-x86_64-3.5/src/lib/random.o:/usr/include/boost/system/detail/error_code.ipp:66: first defined here
build/temp.linux-x86_64-3.5/src/lib/non_cache.o:(.bss+0x0): multiple definition of `boost::system::throws'
build/temp.linux-x86_64-3.5/src/lib/random.o:/usr/include/boost/system/detail/error_code.ipp:66: first defined here
build/temp.linux-x86_64-3.5/src/lib/mutate.o:(.bss+0x0): multiple definition of `boost::system::throws'
build/temp.linux-x86_64-3.5/src/lib/random.o:/usr/include/boost/system/detail/error_code.ipp:66: first defined here
build/temp.linux-x86_64-3.5/src/lib/szv_grid.o:(.bss+0x0): multiple definition of `boost::system::throws'
build/temp.linux-x86_64-3.5/src/lib/random.o:/usr/include/boost/system/detail/error_code.ipp:66: first defined here
build/temp.linux-x86_64-3.5/src/lib/quasi_newton.o:(.bss+0x0): multiple definition of `boost::system::throws'
build/temp.linux-x86_64-3.5/src/lib/random.o:/usr/include/boost/system/detail/error_code.ipp:66: first defined here
build/temp.linux-x86_64-3.5/src/lib/parallel_progress.o:(.bss+0x0): multiple definition of `boost::system::throws'
build/temp.linux-x86_64-3.5/src/lib/random.o:/usr/include/boost/system/detail/error_code.ipp:66: first defined here
build/temp.linux-x86_64-3.5/src/lib/model.o:(.bss+0x0): multiple definition of `boost::system::throws'
build/temp.linux-x86_64-3.5/src/lib/random.o:/usr/include/boost/system/detail/error_code.ipp:66: first defined here
build/temp.linux-x86_64-3.5/src/lib/coords.o:(.bss+0x0): multiple definition of `boost::system::throws'
build/temp.linux-x86_64-3.5/src/lib/random.o:/usr/include/boost/system/detail/error_code.ipp:66: first defined here
build/temp.linux-x86_64-3.5/src/lib/ad4cache.o:(.bss+0x0): multiple definition of `boost::system::throws'
build/temp.linux-x86_64-3.5/src/lib/random.o:/usr/include/boost/system/detail/error_code.ipp:66: first defined here
build/temp.linux-x86_64-3.5/src/lib/grid.o:(.bss+0x0): multiple definition of `boost::system::throws'
build/temp.linux-x86_64-3.5/src/lib/random.o:/usr/include/boost/system/detail/error_code.ipp:66: first defined here
build/temp.linux-x86_64-3.5/src/lib/parallel_mc.o:(.bss+0x0): multiple definition of `boost::system::throws'
build/temp.linux-x86_64-3.5/src/lib/random.o:/usr/include/boost/system/detail/error_code.ipp:66: first defined here
build/temp.linux-x86_64-3.5/src/lib/conf_independent.o:(.bss+0x0): multiple definition of `boost::system::throws'
build/temp.linux-x86_64-3.5/src/lib/random.o:/usr/include/boost/system/detail/error_code.ipp:66: first defined here
build/temp.linux-x86_64-3.5/src/lib/parse_pdbqt.o:(.bss+0x0): multiple definition of `boost::system::throws'
build/temp.linux-x86_64-3.5/src/lib/random.o:/usr/include/boost/system/detail/error_code.ipp:66: first defined here
build/temp.linux-x86_64-3.5/src/lib/cache.o:(.bss+0x0): multiple definition of `boost::system::throws'
build/temp.linux-x86_64-3.5/src/lib/random.o:/usr/include/boost/system/detail/error_code.ipp:66: first defined here
build/temp.linux-x86_64-3.5/vina/autodock_vina_wrap.o:(.bss+0x0): multiple definition of `boost::system::throws'
build/temp.linux-x86_64-3.5/src/lib/random.o:/usr/include/boost/system/detail/error_code.ipp:66: first defined here
collect2: error: ld returned 1 exit status

It would be amazing, if someone can point me to my mistakes.

Thank you very much,
Georg

Dear sscb-scrippts team.

I'm building AutoDock-Vina from source using the 1.2.2 release tarball.

When building the python bindings, the function find_version() fails. Neither version.py nor init.py are included the tarball.

Checking out the git source and building from within the source tree works fine.

This also seems to impact installation via pip.

Hope that's useful.

David

issued the following comand
#vina12 i renamed and put it in the folder
#the config file contains receptor ligand info

"receptor=rec.pdbqt
ligand=lig.pdbqt
center_x = 27.898
center_y = 5.175
center_z = 59.160
size_x = 25
size_y = 25
size_z = 25
exhaustiveness=50"

./vina12 --config config.txt --maps rec.*.map --scoring vinardo --out lig_out.pdbqt --cpu 8
Command line parse error: too many positional options have been specified on the command line

Can I dock a ligand to Zn binding protein using vina not autodock4? and how?

Dear author,

thanks for your great package, however, when i use vina,

v = Vina(sf_name='vina')
v.set_receptor(rigid_pdbqt_filename=xxx)

it get the error

"terminate called after throwing an instance of 'parse_error'
Aborted (core dumped)",

do you know what is the reason? thanks

Dear authors,

Thanks for your great work.

When I use the python wrapper (https://github.com/ccsb-scripps/AutoDock-Vina/tree/boost-python/build/python), I wonder if I could get access to the pose of ligand after v.optimize() instead of using v.dock()?

Thanks!

When I download the Mac OS file and try to open, I get an error that says I don't have any applications to open this type of file. I've tried following online tutorials for installation but they're older so the files are different (from before the Vina website changed) and I'm not sure where to go from here

Hi,

I installed the vina using the commands in AutoDock Vina installation in a Conda environment section in https://autodock-vina.readthedocs.io/en/latest/installation.html on ubuntu-18.04 but vina doesn't work. What could be the problem?

Thanks.

Why you put forcefield.cpp in the lib if you don't want to compile it? Is it part of the lib?

I was using the input files provided in the repository (basic docking), and got the following result:
Scoring function : vina
Rigid receptor: receptors/1iep_receptor.pdbqt
Ligand: ligands/1iep_ligand.pdbqt
Center: X 15.19 Y 53.903 Z 16.917
Size: X 20 Y 20 Z 20
Grid space: 0.375
Exhaustiveness: 32
CPU: 0
Verbosity: 1

Computing Vina grid ... done.
Performing docking (random seed: -131415392) ...
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|

mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -13.62 0 0
2 -12.77 1.136 1.451
3 -9.877 2.853 13.45
4 -9.808 1.766 13.59
5 -9.453 1.86 13.33
6 -8.454 1.317 1.902
7 -8.367 3.759 6.488
8 -8.291 1.864 13.6
9 -8.054 3.032 5.982

At the same time, the pdbqt file generated by the python package has the best docking score (using the same seed) as -14.628

Hello,
I was trying to rigid dock with ad4 scoring function on python script.
The tutorial seems like that by changing scoring function's name, it is possible to use ad4 with rigid docking
However, it gave the error

from vina import Vina
v = Vina(sf_name="ad4")

v.set_receptor("./protein.pdbqt")
v.set_ligand_from_file("./ligand.pdbqt")
v.compute_vina_maps(center=[10.4, 6.9, 27.3], box_size=[20, 20, 20])
energy = v.score()
print(energy[0])

ERROR: Only flexible residues allowed with the AD4 scoring function. No (rigid) receptor.

It works well on other sf such as vina or vinardo.

Is it impossible to use sf ad4 on rigid docking?

Thanks

Hi there,
I have a Mac with M1 Pro and a Windows PC. Tried to install vina on Windows but the installation failed.
Then tried to install vina on Mac and successfully installed vina with Python 3.7.
Vina executable is working for 1.1.2 but not for 1.2.3
Tried installing ADFR, but it errored out when running the .py

(base) tanzibin@ZibinsMacBookPro vina % prepare_receptor -r 1iep_receptorH.pdb -o 1iep_receptor.pdbqt Traceback (most recent call last): File "/Users/tanzibin/ADFR/CCSBpckgs/AutoDockTools/Utilities24/prepare_receptor4.py", line 150, in <module> mol = mols[0] TypeError: 'NoneType' object has no attribute '__getitem__'

(base) tanzibin@ZibinsMacBookPro vina % conda activate vina (vina) tanzibin@ZibinsMacBookPro vina % mk_prepare_ligand.py -i 1iep_ligand.sdf -o 1iep_ligand.pdbqt --pH 7.4 Traceback (most recent call last): File "/Users/tanzibin/opt/anaconda3/envs/vina/bin/mk_prepare_ligand.py", line 13, in <module> from meeko import MoleculePreparation File "/Users/tanzibin/opt/anaconda3/envs/vina/lib/python3.7/site-packages/meeko/__init__.py", line 7, in <module> from .preparation import MoleculePreparation File "/Users/tanzibin/opt/anaconda3/envs/vina/lib/python3.7/site-packages/meeko/preparation.py", line 19, in <module> from .writer import PDBQTWriterLegacy File "/Users/tanzibin/opt/anaconda3/envs/vina/lib/python3.7/site-packages/meeko/writer.py", line 12, in <module> from rdkit import Chem ModuleNotFoundError: No module named 'rdkit'

Any idea?

Thanks

Hi Autodock Vina forum,
We are trying to switch from original Autodock 4.2.6 version to new Autodock Vina 1.2.2 version. To preserve continuity of our calculations, we have chosen to employ AD4 scoring function as implemented in Autodock Vina 1.2.2 with the following command.

"$Vina"/build/linux/release/vina --ligand $ligand.pdbqt --maps ${protein} --scoring ad4 --exhaustiveness 40 --out ${ligand}_${protein}ad4_total.pdbqt >> ${ligand}${protein}_ad4_log.txt
(where variables ligand and protein are substitutes for the working structures).

However, upon test runs of 48 randomly selected compounds from an external database with various settings of exhaustiveness, we have arrived at somewhat confusing results. For each “docking run” there were several compounds with positive docking score whose predicted binding poses were as expected, that is, compound was found in the active site cavity without any overlap of ligand/protein atoms. Furthermore, these positive scores appear to be completely randomized as they can occur at certain exhaustiveness settings, only to disappear for others (see attached file Vina_AD4_scoring_results.xls). We have tried the docking with increased grid box size without any specific improvement. All ligands contain standard atom types that are recognized by the forcefield as evidenced by the fact that no compound has failed at all exhaustiveness settings.
Is there something that we are doing wrong? Or is this perhaps an issue that has already been raised/encountered by someone else?
Thank you for your answer.
##########
Autodock vina version:
1.2.2
downloaded 16 of August 2021, built from source according to installation.rst present in the downloaded file
Operating system and version:
Debian GNU/linux 9
##########
Attached files:
Vina_AD4_scoring_results.xls (results in question are highlighted for your convenience)
Vina_AD4_docking_results.xlsx

How do you use the batch function when docking many ligands in python? The documentation briefly mentions the option of using batch mode for virtual screening, but doesn't seem to explain how to use it.

I tried to follow the latest document. tutorial for preparing the ligand. After installing the Meeko as mentioned, I cannot prepare the ligand as suggested with the following message:

usage: mk_prepare_ligand.py [-h] [-c CONFIG_FILE] -i INPUT_MOLECULE_FILENAME
[-m] [-w] [--keep_nonpolar_hydrogens]
[--pH PH_VALUE] [-f] [-r SMARTS]
[-b i j [i j ...]] [-a] [-p ATOM_TYPE_SMARTS_JSON]
[--double_bond_penalty DOUBLE_BOND_PENALTY]
[--remove_index_map] [--remove_smiles]
[-o OUTPUT_PDBQT_FILENAME]
[--multimol_outdir MULTIMOL_OUTPUT_DIRECTORY]
[--multimol_prefix MULTIMOL_PREFIX] [-v] [-]
mk_prepare_ligand.py: error: unrecognized arguments: --add_hydrogen

Hi,

When I'm trying to use the vinardo ff, it gives following error:

ERROR: Cannot score the pose. Affinity maps were not initialized.

My command: ~/vina_1.2.0_linux_x86_64 --ligand ligand.pdbqt --receptor protein.pdbqt --center_x 15.495 --center_y 2.367 --center_z 15.477 --size_x 20 --size_y 20 --size_z 20 --out vina.pdbqt --score_only --scoring vinardo

Same command works for vina scoring function.

Any help would be appreaciated!

Beset,
Lin

Hi,
I am trying to install vina by creating an environment on Ubuntu 20.04.

conda create -n vina python=3
conda activate vina
python -m pip install --upgrade pip
pip install vina

However, I am facing some installation errors with pip. A complete error file is attached here.

Failed to build vina
ERROR: Could not build wheels for vina, which is required to install pyproject.toml-based projects

error.log

I tried to download the Setup.exe through this website https://vina.scripps.edu/downloads/
but the download page shows nothing except a test.exe which is not executive anyway.

Adding the required Boost projects from https://github.com/boostorg as git submodules would:

• Free the user from installing Boost himself
• Allow easy swap of Boost versions being used

Hello
I have started working on multiple ligands docking while running sample data provided here. On Step Running autodock vina using autodock4 forcefield (--ligand 5x72_ligand_p59.pdbqt 5x72_ligand_p69.pdbqt --maps 5x72_receptor)
I got the error mentioned below
Command line parse error: unknown option maps
Please help, what is wrong

Support of simultaneous docking of multiple ligands and batch mode for virtual screening

I am trying to dock multiple ligands using --batch option. My understanding is that input .pdbqt file for this to work should contain multiple ligands following the pattern below:

MODEL 1
... molecule 1 ...
ENDMDL
MODEL 2
... molecule 2 ...
ENDMDL

Maybe my understanding is not correct and some other mechanism should be used or there is a bug, since when I give a .pdbqt file with multiple ligands as an input it fails with "An unknown error occurred" error message.

I attached vina-An-unknown-error-occurred-bug.tar.gz file which should allow to reproduce the issue.
vina-An-unknown-error-occurred-bug.tar.gz

When running this command:

pythonsh prepare_flexreceptor4.py -r 1fpu_receptor.pdbqt -s THR315 from https://autodock-vina.readthedocs.io/en/latest/docking_flexible.html, I get the WARNING: no residue named THR315 and an empty 1fpu_receptor_flex.pdbqt file.

I copied the 1fpu_receptor.pdbqt file directly from <autodock-vina_directory>/example/flexible_docking/solution and I see the correct 1fpu_receptor_flex.pdbqt in the directory that includes THR315 as flexible. Could you kindly assist me fixing this issue?

Hi,

I'm trying to load existing maps for vina and only score the pose with the following code, but it terminated with "Reading Vina maps ... Segmentation fault".

~/vina_1.2.2_linux_x86_64 --ligand 3ozt_105.pdbqt --maps 3ozt_protein --scoring vina --score_only

The maps were previously generated by command:

/opt/software/MGLTools/1.5.6/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py -l 3ozt_105.pdbqt -r 3ozt_protein.pdbqt -o 3ozt_protein.gpf -y
autogrid4 -p 3ozt_protein.gpf -l grid.log

Could you help to debug?

Thanks!
Best,
Lin

Dear,
when i tried to run the example $ vina --receptor 5x72_receptor.pdbqt --ligand 5x72_ligand_p59.pdbqt 5x72_ligand_p69.pdbqt
--config 5x72_receptor_vina_box.txt
--exhaustiveness 32 --out 5x72_ligand_vina_out.pdbqt

turned out as Command line parse error: too many positional options have been specified on the command line

but when I just run the single ligand, that's totally fine

can you help me with it? thanks

I have MacBook Air (M1,2020)
macOS Monterey 12.0.1

I downloaded vina_1.2.3_mac_x86_64 and tried to run it from the terminal with "./vina_1.2.3_mac_x86_64", but it is not running. Same with vina_1.2.2_macos_arm64. When I extracted the info, it showed that it was a document file. I'm guessing it should show " Unix Executable File " but it doesn't. I tried all of the other releases available on github and encountered the same problem.

I also followed solution by @atillack issue #14 but no success. Below is the screenshot.

I downloaded Vina for Mac from the old site a few months ago, and it works perfectly. How to resolve it?

Hi, I am working with flexible docking, and compared to nonflexible docking it is giving very high scores: 2252099169.975 kcal/mol and is taking very long to run per protein. Could you kindly tell me what is issue with this docking?

Receptor: https://alphafold.ebi.ac.uk/entry/P29699
Ligand: https://pubchem.ncbi.nlm.nih.gov/compound/Ergothioneine

Let me know if providing the code I used would be helpful.

Hi,

I was trying out Vina's Python API as in this example in jupyter notebook. When I run the line v.set_receptor(ligand_path), the kernel restarts.

The error message shown is The kernel appears to have died. It will restart automatically.

Thanks,
Arun

Dear author,
Thank you for the AutoDock Vina 1.2!
I've run docking for about 1700 ligands using your vina python module and most of them was successfully docked but 9 had a problem with the command v.set_ligand_from_file('someid.pdbqt'), it gives "terminate called after throwing an instance of 'stream_parse_error' ".
The most inconvenient thing when it happens the error does not give traceback and interrupt program but just freezes it.
Version info:
Python 3.7
Open Babel 3.1.0
vina 1.2.0.dev3
The code is:

v = Vina(sf_name='vina', cpu=32, seed=1024, no_refine=False, verbosity=1)
v.set_receptor(rigid_pdbqt_filename='receptor.pdbqt')
v.set_ligand_from_file('someid.pdbqt')
v.compute_vina_maps(center=[x, y, z], box_size=[x_size, y_size, z_size], spacing=1)
v.dock(exhaustiveness=32, n_poses=9)
v.write_poses(pdbqt_filename=output, overwrite=True)

Also I tried to run this problem ligands using binaries and it gives error "An unknown error occurred.".
Pdbqt convertation was done by the command mk_prepare_ligand.py -i someid.sdf -m -o someid.pdbqt
Additional question is - can I use -m flag not only for the preparing the macrocyclic but for all ligands?
Because I have a set of the ligands and only part of them are macrocyclic.
Ligand files are attached in the pdbqt and sdf formats:
pdbqt.zip
sdf.zip

Could you help me please?

Hi,

I am trying to switch over from autodock vina 1.1.2 CLI to the new 1.2.2 version. I have found that the affinities reported when using flexible side chains are very different to both 1.1.2 and to a fully rigid approach in 1.2.2 (5.0 vs 2.5 vs 2.5 kcal/mol). The side chains do not move much and the poses are in very similar positions, but their energies are very different.

It will take me a little time to prepare data that I can post here, so I am also seeing if your team know of anything we could be doing wrong.

Many thanks!

Sorry, man, I have to ask one more silly question. When I do mk_preprare_ligand.py function, returned back as

No module named 'openbabel',

but I already installed openbabel. And it worked well by using openbabel function directly, like obabel ixx.pdb oxx.pdbqt. But the directly converted pdbqt cannot perform docking, errors like this

Command line parse error: unrecognised option

Really appreciated your kindly help, bests.

I am experiencing a problem installing Vina 1.2 in Ubuntu 20.04 LTS. After the step where in I need to input "python setup.py build install", this error showed.

File "setup.py", line 280
sep='\n')
^
SyntaxError: invalid syntax

Upon checking the entire code it says os.path.sep but it also did not work either.

I will appreciate your help. Thanks.

Joanna

When batch mode is used on Linux terminal with a pattern with wild card, it works perfectly file. For example, If I have multiple ligands like ligand1.pdbqt, ligand2.pdbqt ligand3.pdbqt etc, just giving --batch ligand*.pdbqt does the job, but when same is used in windows command prompt, it looks for a file named ligand*.pdbqt and fails to run. How can this be done in windows without having to type names of all the ligands?