Fantastic tutorial on AutoDock Vina! Clear explanations and step-by-step instructions make molecular docking easy to understand. Thank you for sharing your expertise!
When we do docking, at the terminal, it said: "swig/python detected a memomry leak of type 'BHtree', no destructor found", and then my docking stopped half way. What does that mean? And what should i do? I'm usjng windows 11, 64-bit system.
The "memory leak of type 'BHtree'" error is related to Python bindings but usually doesn't stop docking. To fix this: Ensure you're using the latest versions of AutoDock Vina and Python (Python 3.7/3.8 is recommended). Check your input files and parameters for errors. Run the terminal as Administrator if on Windows. If the issue persists, try reinstalling Vina or running it in a clean environment. Let me know if you need further help! 😊
Thank you for the tutorial, sir, I would like to ask because I'm new to molecular docking, If the protein has macromolecules, should I remove the macromolecules too or not? Thank you for sharing
You're welcome! If the macromolecules in your protein structure are not part of the binding site or relevant to the docking process, it's a good practice to remove them. This helps focus the docking calculations on the actual binding interactions between the ligand and the protein. However, if those macromolecules are crucial for maintaining the protein's structural integrity or are involved in the binding site, you might need to keep them. It ultimately depends on the specifics of your study. Let me know if you need further clarification! 😊
Fpocket and AutoDock are great for identifying binding pockets and docking ligands, but they aren't typically used for de novo drug design. For that, consider tools like Schrödinger’s Glide, MOE, or LigBuilder. However, you can still use Fpocket and AutoDock to identify and validate potential binding sites for your new compounds.
first of all thank you for this informative video and please i have a qst why when i writ log=log.txt in my config.txt i do not have result but when i delete it i have result but without log.txt and the later sentence writnig output
Hi, Thanks for connecting with me! If the log= log=log.txt line in your config.txt file is not useful for you, you can add a log file to your command to execute Vina for molecular docking. To do this, use the following command: vina.exe --config conf.txt --log log.txt Replace log.txt with the name of the log file that you want to create. Please let me know if this is helpful.
hello sir, I tried to follow your steps as you had stated in the video for docking between IDH2 and enasidenib. However, the result of the docking score is not the same as how it should have been, which is -14.8. Do you know what might have gone wrong?
Hello @tasnimnajihah1139, docking scores can vary due to differences in parameters, input files, or system settings. Ensure that: The protein and ligand are prepared correctly (e.g., charges, protonation states). The grid box dimensions and center match the tutorial. The same version of AutoDock Vina is used. If everything checks out, slight variations are normal, but significant differences may require revisiting the setup. Let me know if you need further help!
It become very easy to learn. But I am facing some problem in command prompt configuration When i am configuring ….it showing error : could not open LIG,pdbqt for reading Please help ……I am having less time to submit my project 🙏
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?
It's not usual.... Generally grid box restricted molecular docking with in the boundaries of grid box. You should identify the issues. It may be structural issues in receptor or wrong selection of grid box location.
Hi. great video. I have a question after finding out the ligands of our protein. the next step of ligand best match is confusing i could not get it. Kindly help me out, please
Hi @javeriyaAyub, glad you found the video helpful! After identifying the ligands for your protein, the next step involves using AutoDock Vina to perform molecular docking. This process helps determine how well the ligands bind to your protein of interest. You'll need to prepare your ligands and protein structures, set up the docking parameters (like grid box size, exhaustiveness), and then run AutoDock Vina to calculate the binding affinities. Feel free to ask more specific questions if you need further assistance!
Hi! To adjust the grid box in AutoDock Vina without using the control button, you can manually set the grid box dimensions in the configuration file. Specify the center and size of the grid box like this: center_x = center_y = center_z = size_x = size_y = size_z = Replace with the appropriate coordinates and dimensions. This method allows precise control over the grid box settings. Let me know if you need further assistance!
@@pytopia5988 Hi! Thanks for your suggestion. Yes, I can definitely consider making tutorials on using Avogadro. Stay tuned for upcoming videos, and feel free to let me know any specific topics you're interested in!
@axonist I'm unable to do last step to write command it has been showing that vina.exe not found and also there are no objects in config file what should I do if you could help me u r prompt response will be appreciated
It sounds like there might be an issue with the installation or configuration of Autodock Vina. First, ensure that the Vina executable file (vina.exe) is properly installed and accessible in your system's PATH. Additionally, double-check your configuration file to ensure that all necessary parameters and objects are properly defined. If the issue persists, consider reinstalling Autodock Vina or consulting the documentation for troubleshooting tips. Let me know if you need further assistance!
Hi @annieonate2306, thank you for your comment! I’m sorry to hear you're having trouble getting the same results. Could you let me know more about the issue? For example: Are you using the same input files and parameters as shown in the tutorial? Are there any specific error messages or unusual outputs in the command prompt? Are you using the same version of AutoDock Vina as mentioned in the video? Feel free to share more details so I can help troubleshoot the problem! 😊
Parse error on line 23 in file "LIG.pdbqt": ATOM syntax incorrect: "B" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive. How do I fix this problem?
To fix the parsing error in AutoDock Vina, replace the invalid atom type "B" with a valid AutoDock Vina atom type in your ligand file ("LIG.pdbqt"). Then retry the docking procedure.
We're removing ligands from crystallographic files to prepare the protein for docking with new ligands. While AlphaFold structures are useful, crystallographic data typically offers higher resolution and experimentally validated conformations, making it preferable for docking studies.
@@Axonist Makes sense but had a couple other questions: In theory, if the Alphafold predicted structure were to highly accurate (let's say it's at least as good as crystallographic data or better now or in the future) wouldn't removing the ligands alter the conformation of the protein in contrast to it's non-bonded state? How significant is this alteration? Also, would really appreciate it if you could point me in the right direction in order to learn a structured approach to using these tools through COLAB. Is this a viable route? Any disadvantages as opposed to just owning the necessary hardware? How do I master CHARMM? I've been banging my head against the wall for the better part of a year and would be really grateful for any guidance you could provide in this regard.
@@AlwaleedHadaidi Thanks for the questions! Ligand Removal Impact: Yes, removing ligands can alter a protein’s conformation since ligands often stabilize specific structures. Alphafold typically predicts unbound states, so this shift can be significant. Using COLAB: COLAB is a great starting point for learning these tools without expensive hardware, though it has computational limits. For larger projects, owning hardware might be better. Learning CHARMM: Start with official tutorials, documentation, and community forums. Persistence is key-every bit of progress counts! Feel free to reach out if you need more help!
@@AlwaleedHadaidi Great questions! Protein Conformation: Removing ligands can indeed alter the protein’s conformation, sometimes significantly, depending on the protein and ligand involved. This is why some studies start with the ligand-bound structure. Using Colab: Colab is a viable option for molecular docking, especially if you lack high-end hardware. It’s a great learning platform but has limitations like session timeouts and restricted memory. Learning CHARMM: Start with the official CHARMM tutorials and practice running simulations. Gradually, dive into research papers and forums to deepen your understanding. Stay persistent-it’s a challenging field, but you’ll improve with time. Good luck!
While exporting the protein.pdb file into .pdbqt extension format, autodoc said: some atom has zero charges. Thus cannot run the docking operation. Can you suggest how to get rid of it?
The zero-charge error usually means some atoms are missing charges. Try these steps: Check the PDB file for proper atom definitions. Add Hydrogens using tools like AutoDockTools. Assign Charges manually in AutoDockTools. Give these a try and see if it resolves the issue!
To identify ligands in predicted structures, you can look for the small molecule or compound that interacts with the protein or receptor in the docking results. In AutoDock Vina, the ligand is typically the smaller, non-protein structure within the binding site of the larger protein structure. You can visualize this using molecular visualization tools like PyMOL or Chimera, which will allow you to clearly see how and where the ligand is binding to the target protein.
Hi! The "could not open config.txt for reading" error means the file is missing or in the wrong place. Try these steps: Ensure config.txt is in the correct directory. Verify the file is named exactly "config.txt". Use the full path to the file in your command: vina --config C:\path\to\your\config.txt Check you have read permissions for the file. Let me know if you need more help!
It seems like the interface you're using might not be configured correctly or is invoking a Python Shell due to a missing file or path issue. Ensure you've installed AutoDockTools properly, and double-check that the Python path is correctly set. If the problem persists, try reinstalling AutoDockTools or running it as an administrator. Let me know if you need more help!
Hi @neelam If you're not seeing the grid option to save in PDBQT format, make sure you’ve correctly set up the grid box in AutoDock Tools. Sometimes, you need to select the macromolecule and set the grid parameters before the option appears. Let me know if that helps!
Thanks for your kind words. The config.txt file in AutoDock Vina contains the parameters and settings for docking simulations. You create this file before running AutoDock Vina, and it serves as a way to organize and define the various options for your docking experiment in a text-based format. receptor = receptor.pdbqt ligand = ligand.pdbqt out = output.pdbqt center_x = 0.0 center_y = 0.0 center_z = 0.0 size_x = 20.0 size_y = 20.0 size_z = 20.0 exhaustiveness = 8
@@Axonist superb sir I've created and run the cmd I got the error "could not open protein.pdbqt for reading" I checked the file name and there is no space too I wonder what mistake I've been committed
I apologize for the delayed response, and I regret any inconvenience caused. I seem to have missed your comment. If you encounter difficulties with molecular docking, kindly send your ligand and protein structure to my email. I will do my best to assist you.@@DiyaAira
@@Axonist Greetings Sir No need to apologize...infact you are helping us by spending your great time. I came over that issue sir... My heartiest gratitude sir
Thank you so much for your kind words! I'm thrilled to hear that you were able to overcome the issue. Your gratitude is truly appreciated, and I'm always here to help if you have any more questions or concerns in the future. Wishing you continued success and smooth sailing ahead!@@DiyaAira
Hi Sir, I faced a problem when installing the software, hoping you can help me out My MGLTools are unable to read the protein i download from PDB and show swig/python detected a memory leak of type 'BHtree *', no destructor found. Please Help
@@AxonistThank you for you reply Sir. However, I'm still unable to read molecule It shows no (0) molecule detected... Is it because I'm using Window 11?
@@jinx3725 The error indicates a memory leak issue in MGLTools. Try these steps: Ensure MGLTools is compatible with Windows 11. Re-download the PDB file. Update MGLTools to the latest version. Verify the PDB file format. If the issue persists, please share the PDB ID, and I'll take a closer look.
Sir, while repairing missing atoms of some large proteins, there is an "TclError: no more menus can be allocated" is being shown. Followed by, application crash. Please enlighten me and help me to solve the issue ASAP. (URGENT)
@@feraliana5284 The "TclError: no more menus can be allocated" often occurs due to memory issues when handling large proteins. Here's how you can fix it: Optimize the structure: Use PyMOL or Chimera to clean up the protein (e.g., remove unnecessary chains or water molecules). Increase memory: Ensure your system has enough RAM or try using a higher-capacity machine. Use command-line: Avoid GUI to reduce memory strain. Hope this helps! Let me know if you need further assistance.
@@Axonist thank you so much for your help, I really appreciate it. However, according to your explanation, I should remove one of two chains in the 4I5I receptor (it has two chains). Then, I'll use this result for MD analysis, which file can I use? In your video the out file only consists of ligands in a different pose, I can not find the file including receptor and ligand. Does it mean I have to process receptors and ligands using another software such as Chimera?
@@feraliana5284 You're welcome! After docking, you'll need to merge the receptor and ligand for MD analysis. Open both the receptor PDB and ligand output in Chimera or PyMOL. Align the ligand in the receptor's binding site based on the docking result. Save the combined structure as a new PDB file. For MD setup, you can also use the Solution Builder option in CHARMM-GUI to prepare the simulation environment for tools like GROMACS, AMBER, NAMD, etc. Let me know if you need further help!
Hi Priya Unfortunately, AutoDock Vina is only available for 32-bit Windows, but you can still use it on a 64-bit Windows operating system. If you encounter any issues during installation or usage, please don't hesitate to reach out in the comment section. I'll do my best to assist you.
once you will get best pose after molecular docking then you can visualize it via discovery studio, UCSF chimera, and Pymol. You can consider this video for it. th-cam.com/video/pBeaXOnVeGM/w-d-xo.html
Hi @thomaskrajeev5608! The config.txt file isn’t included in the default downloads; it’s a file you need to create yourself to set the docking parameters. In the tutorial, I explain how to write it step by step. Here’s the basic format for the config.txt file: receptor = receptor.pdbqt ligand = ligand.pdbqt center_x = 0 center_y = 0 center_z = 0 size_x = 20 size_y = 20 size_z = 20 exhaustiveness = 8 your command might look like this: vina --config config.txt --out output.pdbqt
Hello, Please take into account the following information for the configuration file. Please open a text file, input the details mentioned below, and save it. You are free to modify the file name and the coordinates of the grid box as needed. receptor = REC.pdbqt ligand = LIG.pdbqt out = docking.pdbqt center_x = center_y = center_z = size_x = size_y = size_z = log = log.txt exhaustiveness = 8
You can try downloading MGLTools from an alternative mirror site or use a different browser. If that doesn't work, consider checking the AutoDock Vina tutorial for additional guidance or solutions.
@@Axonist file name and path are correct I don't know where I'm doing wrong, I have a research project for my bachelors in chemistry and I really want this to work and I need help
# Config file for AutoDock Vina # receptor file receptor = receptor.pdbqt # ligand file ligand = ligand.pdbqt # output file out = output.pdbqt # exhaustiveness of the search (higher is slower but more thorough) exhaustiveness = 8 # number of binding modes to generate num_modes = 9 # energy range for identifying good binding modes energy_range = 3
You can try the following steps: Ensure the folder you're pasting into has the necessary permissions. Right-click the folder, select "Properties," go to the "Security" tab, and ensure your user has "Write" access. Run the file explorer as an administrator and try pasting again.
Try reinstalling AutoDock Tools or check if the installation is complete; ensure you're following the tutorial steps correctly, as configuration files should generate automatically.
Memory leaks when repairing missing atoms can be tricky. Here are some quick tips: Ensure AutoDock Vina and all dependencies are up to date. Verify they are correctly prepared. Break down the process to isolate the issue. Use tools to track memory usage. Hope this helps! Feel free to share more details if you need further assistance.
In this tutorial, Autodock Vina was not utilized with DLG files. However, you have the flexibility to employ various visualizers such as UCSF Chimera, PyMOL, and Discovery Studio for the visualization of heteroatoms.
"Hi @neelam5100! To create a config.txt file, open a text editor (like Notepad), and add the necessary parameters: receptor, ligand, center_x, center_y, center_z, and size_x, size_y, size_z. Save the file as config.txt in the same folder as your docking files. Let me know if you need more help!"
Thank you for your feedback! I appreciate your input regarding the background music. I'll take that into consideration for future content and ensure that it doesn't detract from the overall experience. Your perspective is valuable in helping me improve.
@@iqrahasan9114 If your target structure isn't visible after uploading for docking, try these steps: Ensure the file is in a supported format (e.g., PDB, MOL2), zoom out or adjust view settings, open the file in another tool to check for corruption, ensure correct settings for visualization, use the latest version of the software, and check if Python is installed, as it's required by some docking software. If the issue persists, provide more details about the software and any error messages. Hope this helps!
Fantastic tutorial on AutoDock Vina! Clear explanations and step-by-step instructions make molecular docking easy to understand.
Thank you for sharing your expertise!
Glad it was helpful!
The most awaited video.🙌
Thank you for your kind words.
When we do docking, at the terminal, it said: "swig/python detected a memomry leak of type 'BHtree', no destructor found", and then my docking stopped half way. What does that mean? And what should i do? I'm usjng windows 11, 64-bit system.
The "memory leak of type 'BHtree'" error is related to Python bindings but usually doesn't stop docking. To fix this:
Ensure you're using the latest versions of AutoDock Vina and Python (Python 3.7/3.8 is recommended).
Check your input files and parameters for errors.
Run the terminal as Administrator if on Windows.
If the issue persists, try reinstalling Vina or running it in a clean environment. Let me know if you need further help! 😊
Simplified and easy explanation...thank you for updating
So nice of you
THANK U VERY MUCH BODY :D Respect from TURKİYE
Thanks for your kind words
Thank you for the tutorial, sir, I would like to ask because I'm new to molecular docking, If the protein has macromolecules, should I remove the macromolecules too or not? Thank you for sharing
You're welcome! If the macromolecules in your protein structure are not part of the binding site or relevant to the docking process, it's a good practice to remove them. This helps focus the docking calculations on the actual binding interactions between the ligand and the protein. However, if those macromolecules are crucial for maintaining the protein's structural integrity or are involved in the binding site, you might need to keep them. It ultimately depends on the specifics of your study. Let me know if you need further clarification! 😊
Best video for learning docking ❤
Thanks for your kind words
Very clear sir. Thank you for the very informative and useful video. 🙏🙏🙏🙏🙏🙏🙏🙏
So nice of you. Thanks for your kind words
Sir plz help, after copying the autodock vina setup and by pasting it I'm not getting the vina.exe file
Please check out vina.exe in the following directory: C:\Program Files (x86)\The Scripps Research Institute\Vina\
Sir in this trajectory there are three files vina, vina license and vina_split But there is no file named vina.exe
Sir is this file named vina is actually vina.exe?
Thank you so much sir. Big fan!!!!!!
So nice of you
Hello😊 Very good video! I have a question : could I use Fpocket and Autodock also for a de novo drug design approach ?
Fpocket and AutoDock are great for identifying binding pockets and docking ligands, but they aren't typically used for de novo drug design. For that, consider tools like Schrödinger’s Glide, MOE, or LigBuilder. However, you can still use Fpocket and AutoDock to identify and validate potential binding sites for your new compounds.
first of all thank you for this informative video and please i have a qst why when i writ log=log.txt in my config.txt i do not have result but when i delete it i have result but without log.txt and the later sentence writnig output
Hi,
Thanks for connecting with me!
If the log= log=log.txt line in your config.txt file is not useful for you, you can add a log file to your command to execute Vina for molecular docking. To do this, use the following command:
vina.exe --config conf.txt --log log.txt
Replace log.txt with the name of the log file that you want to create.
Please let me know if this is helpful.
Please consider following command.
vina.exe --config config.txt --log log.txt
OR
vina --config config.txt --log log.txt
hello sir, I tried to follow your steps as you had stated in the video for docking between IDH2 and enasidenib. However, the result of the docking score is not the same as how it should have been, which is -14.8. Do you know what might have gone wrong?
Hello @tasnimnajihah1139, docking scores can vary due to differences in parameters, input files, or system settings. Ensure that:
The protein and ligand are prepared correctly (e.g., charges, protonation states).
The grid box dimensions and center match the tutorial.
The same version of AutoDock Vina is used.
If everything checks out, slight variations are normal, but significant differences may require revisiting the setup. Let me know if you need further help!
It become very easy to learn.
But I am facing some problem in command prompt configuration
When i am configuring ….it showing error : could not open LIG,pdbqt for reading
Please help ……I am having less time to submit my project 🙏
Please share your ligand and receptor file on my email. I try to help you as much as possible.
@@Axonist what is your mail id sir
@@Axonist please provide your mail sir
@Axonist what is your mail
axonistofficial@gmail.com@@aryansingh4421
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?
It's not usual.... Generally grid box restricted molecular docking with in the boundaries of grid box. You should identify the issues. It may be structural issues in receptor or wrong selection of grid box location.
Hi. great video. I have a question after finding out the ligands of our protein. the next step of ligand best match is confusing i could not get it. Kindly help me out,
please
Hi @javeriyaAyub, glad you found the video helpful! After identifying the ligands for your protein, the next step involves using AutoDock Vina to perform molecular docking. This process helps determine how well the ligands bind to your protein of interest. You'll need to prepare your ligands and protein structures, set up the docking parameters (like grid box size, exhaustiveness), and then run AutoDock Vina to calculate the binding affinities. Feel free to ask more specific questions if you need further assistance!
Good evening sir, may I ask how to adjust the grid box, i just can't seem to use the control button 1
Hi! To adjust the grid box in AutoDock Vina without using the control button, you can manually set the grid box dimensions in the configuration file. Specify the center and size of the grid box like this:
center_x =
center_y =
center_z =
size_x =
size_y =
size_z =
Replace with the appropriate coordinates and dimensions. This method allows precise control over the grid box settings.
Let me know if you need further assistance!
sir, if ligand that i use is modification structure amoxicilin, there any preparation to do it? or maybe there any option?
You should minimise the energy of the ligand and then perform molecular docking
@@Axonist using avogadro? can u make tutorials sir?
@@pytopia5988 Noted. I will try to cover avogadro tutorial in upcoming videos.
@@pytopia5988 Hi! Thanks for your suggestion. Yes, I can definitely consider making tutorials on using Avogadro. Stay tuned for upcoming videos, and feel free to let me know any specific topics you're interested in!
@axonist I'm unable to do last step to write command it has been showing that vina.exe not found and also there are no objects in config file what should I do if you could help me u r prompt response will be appreciated
It sounds like there might be an issue with the installation or configuration of Autodock Vina. First, ensure that the Vina executable file (vina.exe) is properly installed and accessible in your system's PATH. Additionally, double-check your configuration file to ensure that all necessary parameters and objects are properly defined. If the issue persists, consider reinstalling Autodock Vina or consulting the documentation for troubleshooting tips. Let me know if you need further assistance!
you should have provided all the links and file in the description box
Thanks for the feedback! All the links and files are already provided in the description box! Let me know if you have any trouble accessing them.
Will it also show output.pdbqt after doing this
It will generate a file named docking.pdbqt based on the configuration specified in the provided config.txt file.
Sir, I can’t get a result just like yours, i followed everything but the cmd give me different result. please hear thank you!
Hi @annieonate2306, thank you for your comment! I’m sorry to hear you're having trouble getting the same results. Could you let me know more about the issue? For example:
Are you using the same input files and parameters as shown in the tutorial?
Are there any specific error messages or unusual outputs in the command prompt?
Are you using the same version of AutoDock Vina as mentioned in the video?
Feel free to share more details so I can help troubleshoot the problem! 😊
Parse error on line 23 in file "LIG.pdbqt": ATOM syntax incorrect: "B" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.
How do I fix this problem?
To fix the parsing error in AutoDock Vina, replace the invalid atom type "B" with a valid AutoDock Vina atom type in your ligand file ("LIG.pdbqt"). Then retry the docking procedure.
Thank you sir very informative
So nice of you
Why are we removing ligands from crystalographic files? Can't we use a protein from the alphafold database?
We're removing ligands from crystallographic files to prepare the protein for docking with new ligands. While AlphaFold structures are useful, crystallographic data typically offers higher resolution and experimentally validated conformations, making it preferable for docking studies.
@@Axonist Makes sense but had a couple other questions:
In theory, if the Alphafold predicted structure were to highly accurate (let's say it's at least as good as crystallographic data or better now or in the future) wouldn't removing the ligands alter the conformation of the protein in contrast to it's non-bonded state? How significant is this alteration?
Also, would really appreciate it if you could point me in the right direction in order to learn a structured approach to using these tools through COLAB. Is this a viable route? Any disadvantages as opposed to just owning the necessary hardware? How do I master CHARMM?
I've been banging my head against the wall for the better part of a year and would be really grateful for any guidance you could provide in this regard.
@@AlwaleedHadaidi Thanks for the questions!
Ligand Removal Impact: Yes, removing ligands can alter a protein’s conformation since ligands often stabilize specific structures. Alphafold typically predicts unbound states, so this shift can be significant.
Using COLAB: COLAB is a great starting point for learning these tools without expensive hardware, though it has computational limits. For larger projects, owning hardware might be better.
Learning CHARMM: Start with official tutorials, documentation, and community forums. Persistence is key-every bit of progress counts!
Feel free to reach out if you need more help!
@@AlwaleedHadaidi Great questions!
Protein Conformation: Removing ligands can indeed alter the protein’s conformation, sometimes significantly, depending on the protein and ligand involved. This is why some studies start with the ligand-bound structure.
Using Colab: Colab is a viable option for molecular docking, especially if you lack high-end hardware. It’s a great learning platform but has limitations like session timeouts and restricted memory.
Learning CHARMM: Start with the official CHARMM tutorials and practice running simulations. Gradually, dive into research papers and forums to deepen your understanding.
Stay persistent-it’s a challenging field, but you’ll improve with time. Good luck!
While exporting the protein.pdb file into .pdbqt extension format, autodoc said: some atom has zero charges. Thus cannot run the docking operation. Can you suggest how to get rid of it?
The zero-charge error usually means some atoms are missing charges. Try these steps:
Check the PDB file for proper atom definitions.
Add Hydrogens using tools like AutoDockTools.
Assign Charges manually in AutoDockTools.
Give these a try and see if it resolves the issue!
how we will identify the ligands in predicted strcutres.
To identify ligands in predicted structures, you can look for the small molecule or compound that interacts with the protein or receptor in the docking results. In AutoDock Vina, the ligand is typically the smaller, non-protein structure within the binding site of the larger protein structure. You can visualize this using molecular visualization tools like PyMOL or Chimera, which will allow you to clearly see how and where the ligand is binding to the target protein.
In command promt its coming as could not open config.txt for reading please give solution
Hi! The "could not open config.txt for reading" error means the file is missing or in the wrong place. Try these steps:
Ensure config.txt is in the correct directory.
Verify the file is named exactly "config.txt".
Use the full path to the file in your command:
vina --config C:\path\to\your\config.txt
Check you have read permissions for the file.
Let me know if you need more help!
I am being directed to Python Shell after clicking on macromolecules and then choosing the option 'choose'. Can you please tell me what is wrong?
It seems like the interface you're using might not be configured correctly or is invoking a Python Shell due to a missing file or path issue. Ensure you've installed AutoDockTools properly, and double-check that the Python path is correctly set. If the problem persists, try reinstalling AutoDockTools or running it as an administrator. Let me know if you need more help!
@@Axonist Thank you so much for your help, I reinstalled the AutoDockTools and now it is working.
@@chanikarkare727 sounds great...Excellent
Sir i cant see the grid option to save in pdbqt format... please help
Hi @neelam If you're not seeing the grid option to save in PDBQT format, make sure you’ve correctly set up the grid box in AutoDock Tools. Sometimes, you need to select the macromolecule and set the grid parameters before the option appears. Let me know if that helps!
Hey sir
Thanks for uploading such a video
May I know how and when to creat config.txt file?
Thanks for your kind words. The config.txt file in AutoDock Vina contains the parameters and settings for docking simulations. You create this file before running AutoDock Vina, and it serves as a way to organize and define the various options for your docking experiment in a text-based format.
receptor = receptor.pdbqt
ligand = ligand.pdbqt
out = output.pdbqt
center_x = 0.0
center_y = 0.0
center_z = 0.0
size_x = 20.0
size_y = 20.0
size_z = 20.0
exhaustiveness = 8
@@Axonist superb sir
I've created and run the cmd I got the error "could not open protein.pdbqt for reading" I checked the file name and there is no space too
I wonder what mistake I've been committed
I apologize for the delayed response, and I regret any inconvenience caused. I seem to have missed your comment. If you encounter difficulties with molecular docking, kindly send your ligand and protein structure to my email. I will do my best to assist you.@@DiyaAira
@@Axonist Greetings Sir
No need to apologize...infact you are helping us by spending your great time.
I came over that issue sir...
My heartiest gratitude sir
Thank you so much for your kind words! I'm thrilled to hear that you were able to overcome the issue. Your gratitude is truly appreciated, and I'm always here to help if you have any more questions or concerns in the future. Wishing you continued success and smooth sailing ahead!@@DiyaAira
Hi Sir, I faced a problem when installing the software, hoping you can help me out
My MGLTools are unable to read the protein i download from PDB and show swig/python detected a memory leak of type 'BHtree *', no destructor found.
Please Help
First uninstall the python and mgltool, and then reinstall it again
@@AxonistThank you for you reply Sir. However, I'm still unable to read molecule It shows no (0) molecule detected... Is it because I'm using Window 11?
@@jinx3725 The error indicates a memory leak issue in MGLTools. Try these steps:
Ensure MGLTools is compatible with Windows 11.
Re-download the PDB file.
Update MGLTools to the latest version.
Verify the PDB file format.
If the issue persists, please share the PDB ID, and I'll take a closer look.
I'm unable to download the chimera bcoz the accept option is not showing for me what can I do now??😢
Please download UCSF Chimera X latest version.
Sir, while repairing missing atoms of some large proteins, there is an "TclError: no more menus can be allocated" is being shown. Followed by, application crash.
Please enlighten me and help me to solve the issue ASAP. (URGENT)
Please share your protein ID or PDB file of your receptor protein, and I'll try to resolve the issue.
@@Axonist I also found the same problem. the receptor is 4I5I
@@feraliana5284 The "TclError: no more menus can be allocated" often occurs due to memory issues when handling large proteins. Here's how you can fix it:
Optimize the structure: Use PyMOL or Chimera to clean up the protein (e.g., remove unnecessary chains or water molecules).
Increase memory: Ensure your system has enough RAM or try using a higher-capacity machine.
Use command-line: Avoid GUI to reduce memory strain.
Hope this helps! Let me know if you need further assistance.
@@Axonist thank you so much for your help, I really appreciate it. However, according to your explanation, I should remove one of two chains in the 4I5I receptor (it has two chains). Then, I'll use this result for MD analysis, which file can I use? In your video the out file only consists of ligands in a different pose, I can not find the file including receptor and ligand. Does it mean I have to process receptors and ligands using another software such as Chimera?
@@feraliana5284
You're welcome! After docking, you'll need to merge the receptor and ligand for MD analysis.
Open both the receptor PDB and ligand output in Chimera or PyMOL.
Align the ligand in the receptor's binding site based on the docking result.
Save the combined structure as a new PDB file.
For MD setup, you can also use the Solution Builder option in CHARMM-GUI to prepare the simulation environment for tools like GROMACS, AMBER, NAMD, etc. Let me know if you need further help!
For windows its available with 32 bit, is it same for windows 64 bit ??
Hi Priya
Unfortunately, AutoDock Vina is only available for 32-bit Windows, but you can still use it on a 64-bit Windows operating system. If you encounter any issues during installation or usage, please don't hesitate to reach out in the comment section. I'll do my best to assist you.
how can i visualise my docked structure after this
once you will get best pose after molecular docking then you can visualize it via discovery studio, UCSF chimera, and Pymol. You can consider this video for it. th-cam.com/video/pBeaXOnVeGM/w-d-xo.html
How to do it with multiple ligands?
This method is only for single protein-ligand interaction. Please consider pyrx for multiple ligands and receptor protein interaction
Well explained sir🙏
Thanks for liking
I downloaded everything but can't find the config.txt file
Hi @thomaskrajeev5608! The config.txt file isn’t included in the default downloads; it’s a file you need to create yourself to set the docking parameters. In the tutorial, I explain how to write it step by step. Here’s the basic format for the config.txt file:
receptor = receptor.pdbqt
ligand = ligand.pdbqt
center_x = 0
center_y = 0
center_z = 0
size_x = 20
size_y = 20
size_z = 20
exhaustiveness = 8
your command might look like this:
vina --config config.txt --out output.pdbqt
hello, i'm not getting "Config" file
can anyone help me with that
Hello,
Please take into account the following information for the configuration file. Please open a text file, input the details mentioned below, and save it. You are free to modify the file name and the coordinates of the grid box as needed.
receptor = REC.pdbqt
ligand = LIG.pdbqt
out = docking.pdbqt
center_x =
center_y =
center_z =
size_x =
size_y =
size_z =
log = log.txt
exhaustiveness = 8
Hello, i can't download the mgltools from the website 😢 how to solve that because i want to use autodock vina
You can try downloading MGLTools from an alternative mirror site or use a different browser. If that doesn't work, consider checking the AutoDock Vina tutorial for additional guidance or solutions.
Excellent 👌🏻
Thanks a lot 😊
Hi, I'm having an error could not open "config.txt" for reading. I've tried everything but still having the same error
Ensure the "config.txt" file path is correct, the file exists, and you have read permissions. Here’s an example "config.txt" file for AutoDock Vina:
receptor = receptor.pdbqt
ligand = ligand.pdbqt
out = output.pdbqt
log = log.txt
center_x = 0
center_y = 0
center_z = 0
size_x = 20
size_y = 20
size_z = 20
exhaustiveness = 8
num_modes = 9
energy_range = 3
Double-check your file name and path, and try again.
@@Axonist file name and path are correct I don't know where I'm doing wrong, I have a research project for my bachelors in chemistry and I really want this to work and I need help
@@shahzaib8922 If possible please share your files on my email, I will try to find out the issues.
@@Axonist sure what's the email
@@shahzaib8922 Checkout channel's about us page
can you tell me how will I get the config.txt file?
# Config file for AutoDock Vina
# receptor file
receptor = receptor.pdbqt
# ligand file
ligand = ligand.pdbqt
# output file
out = output.pdbqt
# exhaustiveness of the search (higher is slower but more thorough)
exhaustiveness = 8
# number of binding modes to generate
num_modes = 9
# energy range for identifying good binding modes
energy_range = 3
Sir my vina.exe file is copied but not paste ni folder wht should i do for this?
You can try the following steps:
Ensure the folder you're pasting into has the necessary permissions.
Right-click the folder, select "Properties," go to the "Security" tab, and ensure your user has "Write" access.
Run the file explorer as an administrator and try pasting again.
my AutoDock tools is not giving the config text file. how can I resolve that, please?
Try reinstalling AutoDock Tools or check if the installation is complete; ensure you're following the tutorial steps correctly, as configuration files should generate automatically.
hello thanks for this tutorial, the last step doesn't work for me. thanks
Please let me know what kind of issue are you facing....
My autodock is not opening. Kindly help me anyone. When i try to open autodock after 8% load it automatically close. What to do? #kindly help
Please uninstall it and again reinstall then it could be resolved the issue
im getting memory leaks when repairing missing atoms...
Memory leaks when repairing missing atoms can be tricky. Here are some quick tips:
Ensure AutoDock Vina and all dependencies are up to date.
Verify they are correctly prepared.
Break down the process to isolate the issue.
Use tools to track memory usage.
Hope this helps! Feel free to share more details if you need further assistance.
@@Axonist thanks for the quick answer, hopefully i can find what caused the problem
I have a system 64 bit but I downloaded 32bit of Autodock Vina will it work please
No, a 32-bit version of AutoDock Vina might not work properly on a 64-bit system. It's recommended to download the 64-bit version for compatibility.
Where can i download for 64 bit?
sir where is DLG file or hetro atom file in word format
In this tutorial, Autodock Vina was not utilized with DLG files. However, you have the flexibility to employ various visualizers such as UCSF Chimera, PyMOL, and Discovery Studio for the visualization of heteroatoms.
Can you make tutorial on MzDOCK
Mzdock is having bugs, once it's stable version will come then I will try to cover it in upcoming video
@@Axonist what is the bug you identified?
@@kinglobby6684 It is not fully compatible with several machine that having windows 11 OS latest version.
@@Axonist are you talking about the new MzDOCK or MZ-DOCK. Did you download MzDOCK from sourceforge
Sir how to make a config.txt file....tell steps
"Hi @neelam5100! To create a config.txt file, open a text editor (like Notepad), and add the necessary parameters: receptor, ligand, center_x, center_y, center_z, and size_x, size_y, size_z. Save the file as config.txt in the same folder as your docking files. Let me know if you need more help!"
Command prompt me error a rahi hai what is the solution
Let me know what kind of error you are getting
Autodock vina not working 😢😢
Please let me know what kind of error you are getting
thanks. but the background music is not necessary, it is distracting
Thank you for your feedback! I appreciate your input regarding the background music. I'll take that into consideration for future content and ensure that it doesn't detract from the overall experience. Your perspective is valuable in helping me improve.
Can you please help me for install autodock vina
Please let me know what kind of issue are you facing for autodock vina installation???
No installation issue.. But when I upload a target for docking structure is not visible on the screen
@@iqrahasan9114 If your target structure isn't visible after uploading for docking, try these steps: Ensure the file is in a supported format (e.g., PDB, MOL2), zoom out or adjust view settings, open the file in another tool to check for corruption, ensure correct settings for visualization, use the latest version of the software, and check if Python is installed, as it's required by some docking software. If the issue persists, provide more details about the software and any error messages. Hope this helps!
@@Axonist can you tell me the.. How all binding sites show by using biovia discovery studio??
@@iqrahasan9114I have already explained this in the following video. Please check it out: th-cam.com/video/pBeaXOnVeGM/w-d-xo.htmlsi=IxPW0rA9pgGmqd9M
🙏
Thanks
👍🏻
Thanks dear