Easy to understand and very helpful. Thank you so much for this tutorial. Hope you continue uploading videos!

Thank you very much, Sir!! I am working on my thesis and since its all online due to the pandemic, I couldn't learn it from my professors but due to your extremely easy to understand videos, I could understand every minute detail within less than 1 hour! Extremely grateful to you Sir! Please keep making such videos. You are a Saviour! I hope the channel receives the love and support it deserves!

Pehli bar kia is like samjhne mai waqt laga sir par practice karu ga kuch aur to aajar ga confidence. Bahot aache se samjhaya hai apne, thankyou sir.

Thank you for explaining every step. For a first time user like myself all the additional steps you included about all the add on programs that needs to be used along with autodock vina is vitally important. Others who use these programs regularly tends to forget to explain the beginning steps like the downloading of autodock tools etc and the command prompt window. This was excellent. Thanks

Thank you sir. You literally saved my life! I hope you every success in your research and life! from Korea ☺

the best tutorial, thank you very much for saving my miserable life. Hope you continue!!

i am having a hard time understanding molecular docking but with your videos I am starting to understand how it works. thank you

Very helpful. These Part 1 and Part 2 videos cover everything from the start to the end for pursuing docking. Thankyou.

Both of your video was easy to learn and your seminar also . I had missed out steps after command prompt in Seminar and now I have completed it , Thank You

This makes so much more sense than my teacher explaining it to me! Thanks a bunch!

Thanks for this easy explication, I am started with docking and your video has the best that I could find. And also I am very gratefully because you have used very clear english

This is very helpful video ..I have my exam after two days and I found out this video ..it helped me

Wow! You are a lifesaver! Been looking for Autodock tutorial video for a while now! Thank you

How to create the config file? This is where I m struggled!

You are AWESOME!!!! I easily could demonstrated the basic with watching your presentation!

Very informative session. And the way you explained is very easy to understand that even a beginner who has no idea on docking can learn easily.. keep it up sir. 👏👏

Seriously the best way ur have explained.. Thank you soo much. But can u please tel us how to view the the results becoz everything is completely done.. Finally I am getting as "ACCESS IS DENIED".

Thank u sir..in IIIT ALLAHABAD faculty also taught like horrible way...u made it so easy sir

after autodoc vena command im getting this Correct usage: Input: --receptor arg rigid part of the receptor (PDBQT) --flex arg flexible side chains, if any (PDBQT) --ligand arg ligand (PDBQT) Search space (required): --center_x arg X coordinate of the center --center_y arg Y coordinate of the center --center_z arg Z coordinate of the center --size_x arg size in the X dimension (Angstroms) --size_y arg size in the Y dimension (Angstroms) --size_z arg size in the Z dimension (Angstroms) Output (optional): --out arg output models (PDBQT), the default is chosen based on the ligand file name --log arg optionally, write log file Misc (optional): --cpu arg the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1) --seed arg explicit random seed --exhaustiveness arg (=8) exhaustiveness of the global search (roughly proportional to time): 1+ --num_modes arg (=9) maximum number of binding modes to generate --energy_range arg (=3) maximum energy difference between the best binding mode and the worst one displayed (kcal/mol) Configuration file (optional): --config arg the above options can be put here Information (optional): --help display usage summary --help_advanced display usage summary with advanced options --version display program version

Most beautiful video ever sir !! I am so excited to learn abt this software and these tools. Explained beautifully. I am so excited to try this tomorrow on my PC 😍 thank you so much sir

beautifully explained sir, this is for one ligand only, what if we have multiple ligands, how to perform docking for multiple ligands in windows.

awesomeeeee ur teaching....am a new growing in this field...this video so much helpful

Very helpful..... Thanks a lot.. This video series helped me a lot in completing my project

Very informative tutorial, but you have mistaken in one thing. AutoDock Vina, in contrast to AutoDock 4, uses different grid box units. Therefore, in order to achieve correct box size you must set spacing parameter to 1.

Hi sir your video is really useful. but while running in the command prompt its showing some error in the config file as it is not correct. Can you please help in sorting it out?

Thank you for the very informative videos, they were easy to understand and made the work easier.

I am new to molecular docking and had been struggling to use autodock vina. I had approached my colleagues and others proficient in its use. However, I must admit that none of them could explain this as lucidly as you did. I appreciate and thank you for your efforts to share your knowledge. As I have mentioned, I am new to autodock and after watching and trying the example elaborated in the tutorial, I have a couple of queries, as posted below. I hope you will try to spare some time to respond to the same. I must admit, these might be trivial but as of now, these are posing a hurdle for me. 1. Is there an alternative to PyMol, like any other free software ? 2. Can we not use autodock tools for visualizing the output.pdbqt file? 3. Under what conditions should we change the parameters specified in the config file? Thanks a lot again.

Thhank you for such helpful video, it helped me how to apply it to my research project :)

Wow m amazed by ur explaining methods ,very well explained...making it look soo simple and easy

C:\docking>"C:\Program Files (x86)\The Scripps Research Institute\Vina\vina.exe"--receptor protein.pdbqt --ligand ligand.pdbqt --config config.txt --log log.txt --out output.pdbqt '"C:\Program Files (x86)\The Scripps Research Institute\Vina\vina.exe"--receptor' is not recognized as an internal or external command, operable program or batch file. can any one answer about what is the problem?

I have been looking for such tutorial, now I got it. This video clear some of my doubts. I would like to know is how to choose the natural compund ligand for protein target.

Nice explanation, just few points here I. As far the official tutorial of Autodock Vina, Grid spacing should be changed to 1.00. 2. This is basically active site docking, to generate unbiased results blind docking should be preferred i.e. covering the whole of the protein within the grid box. Would appreciate your response in this two points. Thank you.

thanks a lot for your explanation!!! just a comment, if you put everything in the config txt file no need to write them again in the cmd promt, only running the --config conf.txt command would be enough.

Great video!!! This video is literally saving my final year project.

Very easily explained. Thank you so much for the video!

very very good video to understand,, very useful specially for beginners

Rapid, clearly and very neatly explained the concepts behind docking. Thank you for the same. But now after docking how am I to interpret this concept in my paper. Can you please give me some suggestions that are to be followed.

Sir, Ur both the videos are very well explained but after entering all the paths in the command prompt, I'm getting a command enlisting that "the scripts research institute is not recognised for internal and external Command operable program or batch file." Sir, pls suggest some way out for this...I'm struggling a lot since last month.

at what time we should create config file. I appreciate it if you show me at what stage we should create it. Please let me know whether I should close the vina when I save the protein file with file extension protein.pdbqt. I saw that when you drag ligand.pdbqt in vina, there was nothing in the screen of vina. Please clarify both. Thanks and have a good evening.

How the autodock predict the active site by itself, most of the times we use the literature to define the binding pocket. Pls explain ur statement in the video

very useful indeed. did my ligand and proteins docking using this video.helpful

Excellent way to explain....very helpful. Thankyou

I wish I could react love :) Amazing video. Very very well explained and helpful.

Such a great effort....no confusions...thanks alot...Ja za kallah hu khair

Just one word, Amazing!

Thank you so much for the amazing and well explained tutorial

Thank you sir for giving such a very important information

Hi , how did you create the config .txt file ?

Or it comes like is not recognized as an internal or external command operable program or batch file

if, I use NotePad rather than wordPad will there any problem to docking?

Thank you so much for this amazing effort

Tysm for this. U made it really easy. Was of great help. Hope your safe.

Thank you so much sir for giving this wonderful explanation

how to create the config file or is it autogenerated

Where did the "config" file come from in the beginning of the video?

I am getting this problem, kindly help me out Input: --receptor arg rigid part of the receptor (PDBQT) --flex arg flexible side chains, if any (PDBQT) --ligand arg ligand (PDBQT) Search space (required): --center_x arg X coordinate of the center --center_y arg Y coordinate of the center --center_z arg Z coordinate of the center --size_x arg size in the X dimension (Angstroms) --size_y arg size in the Y dimension (Angstroms) --size_z arg size in the Z dimension (Angstroms) Output (optional): --out arg output models (PDBQT), the default is chosen based on the ligand file name --log arg optionally, write log file Misc (optional): --cpu arg the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1) --seed arg explicit random seed --exhaustiveness arg (=8) exhaustiveness of the global search (roughly proportional to time): 1+ --num_modes arg (=9) maximum number of binding modes to generate --energy_range arg (=3) maximum energy difference between the best binding mode and the worst one displayed (kcal/mol) Configuration file (optional): --config arg the above options can be put here Information (optional): --help display usage summary --help_advanced display usage summary with advanced options --version display program version C:\vina>

Thank you very much for the video. It's easy to understand and get acquainted.

i am unable to do the dockig. When I am adding to command prompt, it is showing access denied. How to resolve it?

Hey I followed the steps but the output file I have obtained is in .txt format and thus I'm not able to open it in pymol. Please help

Many thanks for this informative tutorial. I followed exactly all steps but always get this message ('C:\Program' is not recognized as an internal or external command, operable program or batch file.) Any help would be greatly appreciated

This is great but how to save the final docked ligand in the protein?

Dear Dr. Sanket, it is indeed a very nice tutorial. Thank you so much! But I got stuck after entering the cmd lines, an error popped up saying “could not open "config.txt" for reading." I have very carefully copied every grid parameter into a workpad named "config.txt". But it still doesn't work. Do you have any idea what mistake I probably made?

While running vina , I am getting following output. Kindly help me how to solve it: C:\vina>vina ..config mof.txt ..log log.txt Command line parse error: too many positional options Correct usage: Input: --receptor arg rigid part of the receptor (PDBQT) --flex arg flexible side chains, if any (PDBQT) --ligand arg ligand (PDBQT) Search space (required): --center_x arg X coordinate of the center --center_y arg Y coordinate of the center --center_z arg Z coordinate of the center --size_x arg size in the X dimension (Angstroms) --size_y arg size in the Y dimension (Angstroms) --size_z arg size in the Z dimension (Angstroms) Output (optional): --out arg output models (PDBQT), the default is chosen based on the ligand file name --log arg optionally, write log file Misc (optional): --cpu arg the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1) --seed arg explicit random seed --exhaustiveness arg (=8) exhaustiveness of the global search (roughly proportional to time): 1+ --num_modes arg (=9) maximum number of binding modes to generate --energy_range arg (=3) maximum energy difference between the best binding mode and the worst one displayed (kcal/mol) Configuration file (optional): --config arg the above options can be put here Information (optional): --help display usage summary --help_advanced display usage summary with advanced options --version display program version C:\vina>

This is wonderful veido helpmed me alot. Can you prepare a vidio how to use Rosseta Design software?

Thank you so much!! both videos were very easy to follow and very understandable!!!

when i comand my confg file its not recongnizing

Sanket Sir in the command prompt it's showing me could not open "protein.pdbqt" for reading. Kindly help me Sir please.

Wonderful tutorial! I'm doing a network pharmacology project and this helped a lot.

How to make the config file?

How to select ligand from databases for practice, For example, if want to do docking of DPP IV and any gliptin? Please help

Hi Sanket, Great video, very well explained. One issue I've been having is that the binding pocket I'm investigating has two Mn(II) ions that are co-ordinated both by the receptor and the ligand when bound. When I process the the receptor through autodock tools, I get a similar error to yours with the notification that there is no charge on the Mn ions. I have tried correcting this directly through editing the pdbqt text but this doesn't seem to have been that effective. It would be really helpful if yourself or anyone else here could shed any light on solving this problem? Cheers.

Thank you very much for this tutorial. I have followed you sequentially but my output is showing error: "could not open protein.pdbqt" for reading

thanks...was quite easy to understand..but getting error after entering docking command in cmd..kindly suggest...

incredibly easy and helpful tutorial Sir👏🏼 Keep it up✌🏼

Thanks for this video, it saved my life!

Thank you so much Great efforts Hats off to you 🙏🏻

Thank you so much!! Very helpful for new user!

Hello sir...when i took a drug molecule as ligand..i got warning tht exhaustiveness value is low..so i changed it to 16....and then got the result...will that be fine if i change the exhaustiveness value????

Thanks for explaining it in a great way

Firstly, Sir the video is very much useful and meaningful. Sir, I had an issue with running command prompt. I followed all the steps properly and when I run the code in command prompt, it runs till the "Analyzing the binding site.... " step and says insufficient memory every time. Actually C drive has enough space. Even then it says insufficient memory. I got the answers 2 to 3 times when I ran it initially and now it says insufficient memory. What to do Sir?

Thank you Sanket B. Your video is very helpful! I have followed your tutorial step by step to try reproduced the output. However, I got a different docking output. My first docking affinity is -5.8 rather than -6.3. Can you explain how this can happen?

Sir your videos are very helpful Thank you so much Sir ❤

Excellent explanation thank you sir...

sir, there is a problem arises in command prompt. the configuration file parse error it shows . please give the solution to this problem

Sir, Thank you so much for your wonderful lesson. Can u let me know if there are any advanced lectures on docking? if no please do upload videos!! Kudos

thanks for your explanation i understand all the content

Hello i have a question What about torsions of ligand. What is the minimum range should we kept torsions angles?

thank you Sir for a beautiful explanation but how you are deleting the exsisting ligand

How to prepare Config text file

i want to find inhibitors for foxo1 protein but the problem is, on RCSB-PDB their is no separate structure for foxo1, all structures are bound to dna so, can use such a protein bound to dna for autodock?

I am docking two proteins together (CISD1-Ub), I am guessing I don't have to add hydrogen atoms to them? or do I follow all the steps for each protein like you did equally?

This tutorial has been really helpful, thank you! I am facing this in command prompt that config file cannot be read. Tried so many things but didn't work out. It just shows the help message or the error. Can I get any help with this?

Can you please tell the properties of pdbqt file like open with pymol, wordpad, notepad, word or ....etc. Pls let me know

Sir can you please tell the process of multiple protein binding to a single ligand

Sir, I'm doing docking and I followed all your steps...but sir I'm getting error when running config file in cmd But sir when I'm deleting energy and exhaustiveness from config file then I'm able to run I.e. 2 binding energy comes WHy this is so sir?

Thank you very much, it is easy to understand, my question is: how can I know the active site?

Thank you so much Sir. Sir can you please make a video on how docking is done in Discovery Studio Client 2016?

Heartfelt thanks for this tutorial.

Thank you so much. The tutorial was perfect and understandable. I want to ask you more about the gridbox. Let's assume that we don't know the binding area how should we configure the gridbox? Another question is by knowing the chemical structure of seliciclib before, if we draw the structure in chemdraw and save it as pdb file, will it be possible for us to use that structure as ligand?

Nice and crisp