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ccsb-scripps / AutoDock-Vina

AutoDock Vina
http://vina.scripps.edu
Apache License 2.0
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Vina API multiple ligand docking, showing no conformation generation #77

Open SynchronyML opened 2 years ago

SynchronyML commented 2 years ago

Hello, I am trying to use Vina's API for multi-ligand docking, but it fails. I try as follows:

  1. Add pdbqt ligand twice
  2. Write to a line to add
  3. Two pdbqts are integrated into one file, and then added at one time, All three attempts above have failed. Since I can't upload the pdbqt file, I write the three separately to the markdown text
from vina import Vina
# 如果你想用AutoDock4 或者Vinardo,可以换为vina，ad4 或者vinardo
v = Vina(sf_name='vina')  # 这个就是创建对象
v.set_receptor('5x72_receptor.pdbqt')

# First Try ： add pdbqt one by one
# v.set_ligand_from_file('5x72_ligand_p59.pdbqt')   
# v.set_ligand_from_file('5x72_ligand_p69.pdbqt')  

# Second  Try ： add two pdbqt at one time
# v.set_ligand_from_file('5x72_ligand_p69.pdbqt','5x72_ligand_p59.pdbqt')  

# Third try： add one pdbqt filename with two ligand ，but stiil failed
v.set_ligand_from_file('111.pdbqt')  # 添加第二个受体

v.compute_vina_maps(center=[-15, 15, 129], box_size=[30, 24, 24])

energy = v.score()
print('Score before minimization: %.3f (kcal/mol)' % energy[0])

energy_minimized = v.optimize()
print('Score after minimization : %.3f (kcal/mol)' % energy_minimized[0])
v.write_poses('1iep_ligand_minimized.pdbqt',energy_range=15, overwrite=True)

v.dock(exhaustiveness=8, n_poses=20)
v.write_poses('vina_out_1.pdbqt', n_poses=5, overwrite=True)

print(v.energies())

========================= Result Blow  ==
Computing Vina grid ... done.
Score before minimization: -17.459 (kcal/mol)
Performing local search ... done.
WARNING: Could not find any poses. No poses were written.  # Question
Score after minimization : -19.316 (kcal/mol)
Performing docking (random seed: 404697249) ...

5x72_ligand_p59.pdbqt and 5x72_ligand_p69.pdbqt can find here.

complex of pdbqt file can find below

REMARK  5 active torsions:
REMARK  status: ('A' for Active; 'I' for Inactive)
REMARK    1  A    between atoms: C_7  and  C_8 
REMARK    2  A    between atoms: C_11  and  C_47 
REMARK    3  A    between atoms: N_18  and  C_19 
REMARK    4  A    between atoms: C_31  and  C_32 
REMARK    5  A    between atoms: N_42  and  C_43 
ROOT
HETATM    1  C   UNK     0     -11.690  15.431 130.142  0.00  0.00     0.218 C 
HETATM    2  N   UNK     0     -13.114  15.953 129.994  0.00  0.00    -0.245 NA
HETATM    3  C   UNK     0     -14.114  15.157 130.569  0.00  0.00     0.080 A 
HETATM    4  C   UNK     0     -15.367  15.086 130.009  0.00  0.00     0.003 A 
HETATM    5  C   UNK     0     -16.354  14.267 130.559  0.00  0.00    -0.002 A 
HETATM    6  C   UNK     0     -16.043  13.520 131.662  0.00  0.00    -0.000 A 
HETATM    7  C   UNK     0     -14.765  13.577 132.210  0.00  0.00     0.006 A 
HETATM    8  C   UNK     0     -13.770  14.348 131.634  0.00  0.00     0.073 A 
HETATM    9  C   UNK     0     -12.541  14.567 132.225  0.00  0.00     0.264 C 
HETATM   10  O   UNK     0     -12.478  14.541 133.443  0.00  0.00    -0.267 OA
HETATM   11  N   UNK     0     -11.542  15.232 131.610  0.00  0.00    -0.274 N 
ENDROOT
BRANCH   4  12
HETATM   12  C   UNK     0     -15.720  15.425 127.030  0.00  0.00     0.069 A 
HETATM   13  C   UNK     0     -14.785  16.441 126.795  0.00  0.00    -0.018 A 
HETATM   14  C   UNK     0     -15.185  17.761 126.816  0.00  0.00    -0.002 A 
HETATM   15  C   UNK     0     -16.514  18.057 127.055  0.00  0.00     0.017 A 
HETATM   16  C   UNK     0     -17.467  17.059 127.333  0.00  0.00     0.061 A 
HETATM   17  C   UNK     0     -17.073  15.733 127.305  0.00  0.00    -0.000 A 
BRANCH  16  18
HETATM   18  N   UNK     0     -18.713  17.495 127.578  0.00  0.00    -0.274 N 
HETATM   19  C   UNK     0     -19.097  17.872 128.953  0.00  0.00     0.218 C 
HETATM   20  N   UNK     0     -20.025  19.036 128.928  0.00  0.00    -0.245 NA
HETATM   21  C   UNK     0     -20.945  19.131 127.899  0.00  0.00     0.083 A 
HETATM   22  C   UNK     0     -22.041  19.951 128.048  0.00  0.00     0.019 A 
HETATM   23  C   UNK     0     -20.758  18.379 126.740  0.00  0.00     0.073 A 
HETATM   24  C   UNK     0     -22.985  20.074 127.024  0.00  0.00     0.002 A 
HETATM   25  C   UNK     0     -22.777  19.369 125.863  0.00  0.00     0.000 A 
HETATM   26  C   UNK     0     -21.659  18.529 125.705  0.00  0.00     0.006 A 
HETATM   27  C   UNK     0     -19.579  17.649 126.567  0.00  0.00     0.264 C 
HETATM   28  O   UNK     0     -19.175  17.344 125.429  0.00  0.00    -0.267 OA
BRANCH  19  29
HETATM   29  C   UNK     0     -19.691  16.745 129.568  0.00  0.00     0.049 A 
HETATM   30  C   UNK     0     -19.752  16.729 130.955  0.00  0.00     0.140 A 
HETATM   31  F   UNK     0     -19.277  17.726 131.586  0.00  0.00    -0.204 F 
HETATM   32  C   UNK     0     -20.305  15.662 131.653  0.00  0.00     0.029 A 
HETATM   33  C   UNK     0     -20.805  14.551 130.997  0.00  0.00     0.002 A 
HETATM   34  C   UNK     0     -20.772  14.540 129.603  0.00  0.00    -0.000 A 
HETATM   35  C   UNK     0     -20.188  15.611 128.891  0.00  0.00     0.002 A 
ENDBRANCH  19  29
ENDBRANCH  16  18
ENDBRANCH   4  12
BRANCH   1  36
HETATM   36  C   UNK     0     -11.336  14.195 129.474  0.00  0.00     0.049 A 
HETATM   37  C   UNK     0     -11.259  14.157 128.075  0.00  0.00     0.140 A 
HETATM   38  F   UNK     0     -11.545  15.278 127.337  0.00  0.00    -0.204 F 
HETATM   39  C   UNK     0     -10.884  12.997 127.399  0.00  0.00     0.029 A 
HETATM   40  C   UNK     0     -10.570  11.852 128.109  0.00  0.00     0.002 A 
HETATM   41  C   UNK     0     -10.650  11.860 129.498  0.00  0.00    -0.000 A 
HETATM   42  C   UNK     0     -11.007  13.015 130.170  0.00  0.00     0.002 A 
ENDBRANCH   1  36
BRANCH  11  43
HETATM   43  C   UNK     0     -10.472  15.747 132.249  0.00  0.00     0.065 A 
HETATM   44  C   UNK     0      -9.228  15.824 131.627  0.00  0.00     0.017 A 
HETATM   45  C   UNK     0      -8.159  16.443 132.293  0.00  0.00     0.002 A 
HETATM   46  C   UNK     0      -8.314  16.976 133.591  0.00  0.00     0.000 A 
HETATM   47  C   UNK     0      -9.564  16.927 134.197  0.00  0.00     0.002 A 
HETATM   48  C   UNK     0     -10.625  16.335 133.514  0.00  0.00     0.017 A 
ENDBRANCH  11  43
TORSDOF 5
diogomart commented 1 year ago

To dock multiple ligands simultaneously from Python pass a list of filenames

filenames = ['5x72_ligand_p69.pdbqt','5x72_ligand_p59.pdbqt']
v.set_ligand_from_file(filenames)