Dear Anurag Makare Use MGLTools for preparing the proteins using the classical method of removing waters, adding protons, adding charges, then defining it as macromolecule and saving it as pdbqt, it will take time since you will have to treat a lot of files, for myself I prefer this method and use it instead of the prepare_receptor.py script, I have used that script and sometimes it gave me invalid outputs, especially with some metalloproteins.

best regards

@Hicham-Mechqoq Sir I actually have 1000s of Proteins so it will not be possible to individually make pdbqt files. I just want to do Molecular Docking with Multiple Proteins. Is there any other way to do it though?

Dear Anurag Makare , I will give you the script I use, try this prepare_receptor.py and tell me if its working better:

#!/usr/bin/env python

import os

import sys

import glob

from subprocess import Popen, PIPE

def check_mgl_library():

if os.path.exists('/Library/MGLTools'):

MGL_LIB = glob.glob('/Library/MGLTools/*')

pythonpath = os.path.join(MGL_LIB[0], 'bin', 'pythonsh')

utilities24 = os.path.join(MGL_LIB[0], 'MGLToolsPckgs', 'AutoDockTools', 'Utilities24')

prep_receptor_script = os.path.join(utilities24, 'prepare_receptor4.py')

return (pythonpath, prep_receptor_script)

else:

raise Exception('The prepare_receptor4.py script cannot be found because MGLTools is not installed.')

def execute_receptor_prep(receptor_pdb, output_pdbqt):

pythonpath, prep_script = check_mgl_library()

args = (pythonpath, prep_script, receptor_pdb, output_pdbqt)

cmd = '%s %s -r %s -o %s -A checkhydrogens' % args

p = Popen(cmd, shell=True, stdout=PIPE)

stdout, stderr = p.communicate()

print 'Done!'

if __name__ == '__main__':

try:

receptor_pdb, output_pdbqt = sys.argv[1:]

execute_receptor_prep(receptor_pdb, output_pdbqt)

except ValueError:

print '\nUsage: prepare_receptor.py \n'

Dear Hicham Mechqoq , I am having this error while using your script. Please tell me how can I resolve this.

Thank you

Traceback (most recent call last):

File "/mnt/d/Download/mgltools/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py", line 204, in

dict=dictionary)

File "/mnt/d/Download/mgltools/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 558, in __init__

version=version, delete_single_nonstd_residues=delete_single_nonstd_residues)

File "/mnt/d/Download/mgltools/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 124, in __init__

self.repairMol(mol, self.repair_type_list)

File "/mnt/d/Download/mgltools/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 179, in repairMol

self.newHs = self.addHydrogens(mol)

File "/mnt/d/Download/mgltools/MGLToolsPckgs/AutoDockTools/MoleculePreparation.py", line 187, in addHydrogens

HB.addHydrogens(mol)

File "/mnt/d/Download/mgltools/MGLToolsPckgs/MolKit/hydrogenBuilder.py", line 61, in addHydrogens

babel.assignHybridization(mol.allAtoms)

File "/mnt/d/Download/mgltools/MGLToolsPckgs/PyBabel/atomTypes.py", line 143, in assignHybridization

self.check_for_amides()

File "/mnt/d/Download/mgltools/MGLToolsPckgs/PyBabel/atomTypes.py", line 511, in check_for_amides

if conn.babel_type=="Cac" or conn.babel_type=="Sox" or \

File "/mnt/d/Download/mgltools/MGLToolsPckgs/MolKit/molecule.py", line 409, in __getattr__

raise AttributeError('member %s not found'%member)

AttributeError: member babel_type not found

Done!