Can be done using Vina but again you need quantum parameters to do that. Check out this paper of mine www.sciencedirect.com/science/article/abs/pii/S0169433220313660
@@BioinfoCopilot Thank you very much for sharing this, it is useful. But since I need to do QM/MM using the MFCC still I dont see how to make the fragments
@@BioinfoCopilot I have many different ligands and one protein.. each ligand will interact at some different place.. there are many active sites present on protein,,,,,so how can I define coordinates .. xyz
I don't think there is a parameter called --log in autodockvina, when i ran this sh script it showed "Command line parse error: unrecognised option '--log' ". I use autodock vina version 1.2.5
where do you find the vina executable file and the vina_screen_get_top . py files. Are they both imperative for the success of the code? I am running the code and getting an error that "SH" is unknown in my terminal so I am assuming it is because I don't have those files. Thanks for the help
Here is the script: #Specify how many ligands you want py #vina_screen_get_top.py 3 (or 5, 7, 10 etc) #! /usr/bin/env python import sys import glob def doit(n): file_names = glob.glob('*.pdbqt') everything = [] failures = [] print('Found', len(file_names), 'pdbqt files') for file_name in file_names: file = open(file_name) lines = file.readlines() file.close() try: line = lines[1] result = float(line.split(':')[1].split()[0]) everything.append([result, file_name]) except: failures.append(file_name) everything.sort(key=lambda x: x[0], reverse=False) part = everything[:n] for p in part: print(f"{p[1]}: {p[0]}") print() if len(failures) > 0: print('WARNING:', len(failures), 'pdbqt files could not be processed') if __name__ == '__main__': doit(int(sys.argv[1]))
Im performing docking on a known active site so i limited the gridbox around the active site only. Some of the conformations i got after docking were outside the grid box. Is that normal?
If you have defined the grid box around active site and set the resolution to 1.000 Angstrom then yes otherwise if you set the resoultion to 0.3 then it will only show the ligands in that grid box.
great video bro. but can you show the script that allows us to prepare the input files? For example, i have 100 proteins, i want to convert them from PDB files to PDBQT files at once.
Good day Dr. I want to ask if multiple ligand can interact with receptor in autodock 4?
No, only possible with Vina.
@@BioinfoCopilot thank you Dr. may I ask for docking between protein-protein interaction, which autodock is suitable?
Cluspro is suitable for protein-protein docking
@@BioinfoCopilot Ok thank you for the respons
Thank you for a very nice tutorial. May you please make a tutorial for performing Molecular Fractionation with Conjugate Cap(MFCC) after docking
Can be done using Vina but again you need quantum parameters to do that. Check out this paper of mine www.sciencedirect.com/science/article/abs/pii/S0169433220313660
@@BioinfoCopilot Thank you very much for sharing this, it is useful. But since I need to do QM/MM using the MFCC still I dont see how to make the fragments
How to make size x y z .. is it standard value
No you have to set it using MGLtools
@@BioinfoCopilot I have many different ligands and one protein.. each ligand will interact at some different place.. there are many active sites present on protein,,,,,so how can I define coordinates .. xyz
I don't think there is a parameter called --log in autodockvina, when i ran this sh script it showed "Command line parse error: unrecognised option '--log' ". I use autodock vina version 1.2.5
Check the manual “Summary Usage” section
vina.scripps.edu/manual/
where do you find the vina executable file and the vina_screen_get_top . py files. Are they both imperative for the success of the code? I am running the code and getting an error that "SH" is unknown in my terminal so I am assuming it is because I don't have those files. Thanks for the help
Here is the script:
#Specify how many ligands you want py #vina_screen_get_top.py 3 (or 5, 7, 10 etc)
#! /usr/bin/env python
import sys
import glob
def doit(n):
file_names = glob.glob('*.pdbqt')
everything = []
failures = []
print('Found', len(file_names), 'pdbqt files')
for file_name in file_names:
file = open(file_name)
lines = file.readlines()
file.close()
try:
line = lines[1]
result = float(line.split(':')[1].split()[0])
everything.append([result, file_name])
except:
failures.append(file_name)
everything.sort(key=lambda x: x[0], reverse=False)
part = everything[:n]
for p in part:
print(f"{p[1]}: {p[0]}")
print()
if len(failures) > 0:
print('WARNING:', len(failures), 'pdbqt files could not be processed')
if __name__ == '__main__':
doit(int(sys.argv[1]))
Im performing docking on a known active site so i limited the gridbox around the active site only. Some of the conformations i got after docking were outside the grid box. Is that normal?
If you have defined the grid box around active site and set the resolution to 1.000 Angstrom then yes otherwise if you set the resoultion to 0.3 then it will only show the ligands in that grid box.
I want to know about ligand ligand docking
May be you try Marvin Sketch or Chemsketch. But why ligand -ligand docking?
great video bro. but can you show the script that allows us to prepare the input files? For example, i have 100 proteins, i want to convert them from PDB files to PDBQT files at once.
I will make a video of that soon. Thanks
How to make .sh script sir
Open a text editor , paste your code and then save it as script.sh