AutoDock Vina Tutorial: Molecular Docking for Beginners

[@TechyBrother-u7z]

Fantastic tutorial on AutoDock Vina! Clear explanations and step-by-step instructions make molecular docking easy to understand. Thank you for sharing your expertise!

[@Axonist]

Glad it was helpful!

[@arundhatibajpai6481]

The most awaited video.🙌

[@Axonist]

Thank you for your kind words.

[@rashmisrivastava7668]

Simplified and easy explanation...thank you for updating

[@Axonist]

So nice of you

[@sakshidawange9838]

Sir plz help, after copying the autodock vina setup and by pasting it I'm not getting the vina.exe file

[@Axonist]

Please check out vina.exe in the following directory: C:\Program Files (x86)\The Scripps Research Institute\Vina\

[@rabiaijaz8757]

Sir in this trajectory there are three files vina, vina license and vina_split But there is no file named vina.exe

[@rabiaijaz8757]

Sir is this file named vina is actually vina.exe?

[@tasnimnajihah1139]

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?

[@Axonist]

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!

[@sachinahire5872]

Best video for learning docking ❤

[@Axonist]

Thanks for your kind words

[@thomaskrajeev5608]

I downloaded everything but can't find the config.txt file

[@rohitchel5679]

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?

[@Axonist]

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.

[@dwyanesagun2360]

Good evening sir, may I ask how to adjust the grid box, i just can't seem to use the control button 1

[@Axonist]

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!

[@divyarana3637]

Very clear sir. Thank you for the very informative and useful video. 🙏🙏🙏🙏🙏🙏🙏🙏

[@Axonist]

So nice of you. Thanks for your kind words

[@dusandimitrievski3095]

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?

[@Axonist]

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.

[@jinx3725]

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

[@Axonist]

First uninstall the python and mgltool, and then reinstall it again

[@jinx3725]

@@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?

[@Axonist]

@@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.

[@javeriyaAyub]

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

[@Axonist]

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!

[@MdMahmodulIslam-v8q]

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?

[@Axonist]

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!

[@chanikarkare727]

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?

[@Axonist]

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!

[@chanikarkare727]

@@Axonist Thank you so much for your help, I reinstalled the AutoDockTools and now it is working.

[@Axonist]

@@chanikarkare727 sounds great...Excellent

[@Aditya-e1x]

Thank you so much sir. Big fan!!!!!!

[@Axonist]

So nice of you

[@janeshiganjid4928]

@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

[@Axonist]

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!

[@aalilouyoussra3365]

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

[@Axonist]

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.

[@Axonist]

Please consider following command. vina.exe --config config.txt --log log.txt OR vina --config config.txt --log log.txt

[@praneethkris2k1]

Will it also show output.pdbqt after doing this

[@Axonist]

It will generate a file named docking.pdbqt based on the configuration specified in the provided config.txt file.

[@aryansingh4421]

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 🙏

[@Axonist]

Please share your ligand and receptor file on my email. I try to help you as much as possible.

[@aryansingh4421]

@@Axonist what is your mail id sir

[@aryansingh4421]

@@Axonist please provide your mail sir

[@aryansingh4421]

@Axonist what is your mail

[@Axonist]

[e-mail]@@aryansingh4421

[@AlwaleedHadaidi]

Why are we removing ligands from crystalographic files? Can't we use a protein from the alphafold database?

[@Axonist]

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.

[@AlwaleedHadaidi]

@@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.

[@Axonist]

@@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!

[@Axonist]

@@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!

[@pytopia5988]

sir, if ligand that i use is modification structure amoxicilin, there any preparation to do it? or maybe there any option?

[@Axonist]

You should minimise the energy of the ligand and then perform molecular docking

[@pytopia5988]

@@Axonist using avogadro? can u make tutorials sir?

[@Axonist]

@@pytopia5988 Noted. I will try to cover avogadro tutorial in upcoming videos.

[@Axonist]

@@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!

[@antonellafinali6315]

Hello😊 Very good video! I have a question : could I use Fpocket and Autodock also for a de novo drug design approach ?

[@Axonist]

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.

[@neelam5100]

Sir i cant see the grid option to save in pdbqt format... please help

[@Axonist]

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!

[@vikrantchaudhary5206]

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)

[@Axonist]

Please share your protein ID or PDB file of your receptor protein, and I'll try to resolve the issue.

[@feraliana5284]

@@Axonist I also found the same problem. the receptor is 4I5I

[@Axonist]

@@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.

[@feraliana5284]

@@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?

[@Axonist]

@@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!

[@anandr2729]

how can i visualise my docked structure after this

[@Axonist]

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. kzbin.info/www/bejne/pnPIkouFo7uYfa8

[@shafnamahaboob4919]

I'm unable to download the chimera bcoz the accept option is not showing for me what can I do now??😢

[@Axonist]

Please download UCSF Chimera X latest version.

[@SUVAJITROY-cr5iv]

Thank you sir very informative

[@Axonist]

So nice of you

[@ofosuhemaajoyce9478]

I have a system 64 bit but I downloaded 32bit of Autodock Vina will it work please

[@Axonist]

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.

[@DivyaSekharRatho]

In command promt its coming as could not open config.txt for reading please give solution

[@Axonist]

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!

[@nurulnisa8683]

Hello, i can't download the mgltools from the website 😢 how to solve that because i want to use autodock vina

[@Axonist]

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.

[@sathyapriya9183]

For windows its available with 32 bit, is it same for windows 64 bit ??

[@Axonist]

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.

[@shivanshuagrawal5654]

you should have provided all the links and file in the description box

[@Axonist]

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.

[@likhithgowdahr4437]

hello, i'm not getting "Config" file can anyone help me with that

[@Axonist]

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

[@rimshahsabir4570]

how we will identify the ligands in predicted strcutres.

[@Axonist]

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.

[@maxars9510]

How to do it with multiple ligands?

[@Axonist]

This method is only for single protein-ligand interaction. Please consider pyrx for multiple ligands and receptor protein interaction

[@shahzaib8922]

Hi, I'm having an error could not open "config.txt" for reading. I've tried everything but still having the same error

[@Axonist]

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.

[@shahzaib8922]

@@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

[@Axonist]

@@shahzaib8922 If possible please share your files on my email, I will try to find out the issues.

[@shahzaib8922]

@@Axonist sure what's the email

[@Axonist]

@@shahzaib8922 Checkout channel's about us page

[@mugendidickson2747]

my AutoDock tools is not giving the config text file. how can I resolve that, please?

[@Axonist]

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.

[@dr.sumanlata8216]

Excellent 👌🏻

[@Axonist]

Thanks a lot 😊

[@RiddhaKar]

can you tell me how will I get the config.txt file?

[@Axonist]

# 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

[@ritikasharma1221]

Sir my vina.exe file is copied but not paste ni folder wht should i do for this?

[@Axonist]

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.

[@jahnavitandon6487]

Well explained sir🙏

[@Axonist]

Thanks for liking

[@nousiparvin7376]

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

[@Axonist]

Please uninstall it and again reinstall then it could be resolved the issue

[@DiyaAira]

Hey sir Thanks for uploading such a video May I know how and when to creat config.txt file?

[@Axonist]

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

[@DiyaAira]

@@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

[@Axonist]

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

[@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

[@Axonist]

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

[@derenjoy3r]

im getting memory leaks when repairing missing atoms...

[@Axonist]

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.

[@derenjoy3r]

@@Axonist thanks for the quick answer, hopefully i can find what caused the problem

[@piyushsinghal8116]

sir where is DLG file or hetro atom file in word format

[@Axonist]

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.

[@neelam5100]

Sir how to make a config.txt file....tell steps

[@Axonist]

"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!"

[@Zouhairmustapha]

hello thanks for this tutorial, the last step doesn't work for me. thanks

[@Axonist]

Please let me know what kind of issue are you facing....

[@ajaypharma3006]

Command prompt me error a rahi hai what is the solution

[@Axonist]

Let me know what kind of error you are getting

[@kinglobby6684]

Can you make tutorial on MzDOCK

[@Axonist]

Mzdock is having bugs, once it's stable version will come then I will try to cover it in upcoming video

[@kinglobby6684]

@@Axonist what is the bug you identified?

[@Axonist]

@@kinglobby6684 It is not fully compatible with several machine that having windows 11 OS latest version.

[@kinglobby6684]

@@Axonist are you talking about the new MzDOCK or MZ-DOCK. Did you download MzDOCK from sourceforge

[@iqrahasan9114]

Can you please help me for install autodock vina

[@Axonist]

Please let me know what kind of issue are you facing for autodock vina installation???

[@iqrahasan9114]

No installation issue.. But when I upload a target for docking structure is not visible on the screen

[@Axonist]

@@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!

[@iqrahasan9114]

@@Axonist can you tell me the.. How all binding sites show by using biovia discovery studio??

[@Axonist]

@@iqrahasan9114I have already explained this in the following video. Please check it out: kzbin.info/www/bejne/pnPIkouFo7uYfa8si=IxPW0rA9pgGmqd9M

[@johnajayi6028]

thanks. but the background music is not necessary, it is distracting

[@Axonist]

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.

[@dadasaheb12377]

Autodock vina not working 😢😢

[@Axonist]

Please let me know what kind of error you are getting

[@shivanisharma7054]

🙏

[@Axonist]

Thanks

[@komalkanyan1677]

👍🏻

[@Axonist]

Thanks dear