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!
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
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
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
Thank you so much sir for this informative and easy to understand tutorial for docking. I was alot confused before coming here and now I am very clear about the docking protocol.
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
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. 👏👏
Thank you so much for your help, sir! You've explained things in a very straightforward manner. I'm curious to see what you've discovered? Any publications?
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".
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.
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.
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.
Thank you very much for your response, I am happy you were able to understand it. Coming to your questions: 1. We can use Chimera instead of Pymol 2. We can visualize output.pdbqt in autodock tool 3. If the pocket region is different then the parameters in config will change. P. S. I use pymol because I am comfortable with it.
Hello sir. I took a trial of docking with VINA, upto the final step it goes smoothly but at the end in command section it shows errors.. i have tried atleast 30 time ..but problem remains same..please guide me..
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????
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.
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.
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?
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.
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.
Make a text file by right click in the empty space on the folder ,choose text, open it then fill it by typing the Data ‘ rename the text file as config
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
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.
Thank you -very informative video! could you please suggest how one can do these steps on mac as well? struggling with it for my project. I have prepared the ligand and protein and know how to use autodock/chimera but can't set up the code on command line mac
Easy to understand and very helpful. Thank you so much for this tutorial. Hope you continue uploading videos!
Thank you !
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!
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
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 sir.
You literally saved my life! I hope you every success in your research and life!
from Korea
☺
This was extremely helpful in my research! It was so simple to understand and you explained it in such an easy way! Thank you so much!
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
the best tutorial, thank you very much for saving my miserable life. Hope you continue!!
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
Wow! You are a lifesaver! Been looking for Autodock tutorial video for a while now! Thank you
Thank you!
incredibly easy and helpful tutorial Sir👏🏼
Keep it up✌🏼
Thank you so much sir for this informative and easy to understand tutorial for docking. I was alot confused before coming here and now I am very clear about the docking protocol.
This is very helpful video ..I have my exam after two days and I found out this video ..it helped me
You are AWESOME!!!! I easily could demonstrated the basic with watching your presentation!
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
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. 👏👏
Very helpful..... Thanks a lot.. This video series helped me a lot in completing my project
Such a great effort....no confusions...thanks alot...Ja za kallah hu khair
Great video!!! This video is literally saving my final year project.
Same!
Mine too
awesomeeeee ur teaching....am a new growing in this field...this video so much helpful
Wow m amazed by ur explaining methods ,very well explained...making it look soo simple and easy
Thank you for the very informative videos, they were easy to understand and made the work easier.
Excellent way to explain....very helpful. Thankyou
very very good video to understand,, very useful specially for beginners
Just one word, Amazing!
Very easily explained. Thank you so much for the video!
Thank you so much for your help, sir! You've explained things in a very straightforward manner. I'm curious to see what you've discovered? Any publications?
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 you, can you tell me where you are getting access denied?
very nice and clear explanation in both parts
Thank you so much for the amazing and well explained tutorial
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.
Thanks for explaining it in a great way
Thank you sir for giving such a very important information
Really good explanation!!!! Just to the point!!
Heartfelt thanks for this tutorial.
very useful indeed. did my ligand and proteins docking using this video.helpful
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.
Hey! Thanks a lot this was useful. I got wrong results after ignoring spacing. Now i set it to 1.
How to prepare Config text file
Thank you very much for the video. It's easy to understand and get acquainted.
Excellent explanation thank you sir...
Thank you so much!! both videos were very easy to follow and very understandable!!!
Thank you for making thing easy. Thanks a lot.
Easy to understand thankyou so much sir
Thank you so much!! Very helpful for new user!
Easy to understand and very helpful.
Tysm for this. U made it really easy. Was of great help. Hope your safe.
Thank you so much for this amazing effort
Thank you so much
Great efforts
Hats off to you 🙏🏻
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.
Thank you very much for your response, I am happy you were able to understand it. Coming to your questions:
1. We can use Chimera instead of Pymol
2. We can visualize output.pdbqt in autodock tool
3. If the pocket region is different then the parameters in config will change.
P. S. I use pymol because I am comfortable with it.
You can use Rasmol as a visualization tool
@@yogeetagoyal2086 No i have been trying it. it cant efficiently do when you opt for surface option in the tab!!
@@amodraghupatibhat6288 read its manual once thoroughly...
@@amodraghupatibhat6288 Pymol also you can use..
Where did the "config" file come from in the beginning of the video?
Thhank you for such helpful video, it helped me how to apply it to my research project :)
Thanks for this video, it saved my life!
Thank you sir.. this video was very helpfull
thanks for your explanation i understand all the content
Sir your videos are very helpful
Thank you so much Sir ❤
Best tutorial on Vina
Nice and crisp
Thank you so much for this. You are a life saver
Thanks a lot for both the videos !!
if, I use NotePad rather than wordPad will there any problem to docking?
Thank you so much sir for giving this wonderful explanation
thank you sir for such a wonderful explanation.keep it up.
Hello sir.
I took a trial of docking with VINA, upto the final step it goes smoothly but at the end in command section it shows errors.. i have tried atleast 30 time ..but problem remains same..please guide me..
I wish I could react love :) Amazing video. Very very well explained and helpful.
Thank you very much, it is easy to understand, my question is: how can I know the active site?
excellent explaination..
Wonderful tutorial! I'm doing a network pharmacology project and this helped a lot.
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????
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.
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.
How to create the config file? This is where I m struggled!
Same here😢
same here
This is great but how to save the final docked ligand in the protein?
THANK YOU SO MUCH FOR THE DETAILED VIDEOS
Hi , how did you create the config .txt file ?
Thank u sir..in IIIT ALLAHABAD faculty also taught like horrible way...u made it so easy sir
thanks a lot. This tutorial is awesome
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?
This is wonderful veido helpmed me alot. Can you prepare a vidio how to use Rosseta Design software?
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.
beautifully explained sir, this is for one ligand only, what if we have multiple ligands, how to perform docking for multiple ligands in windows.
Great tutorial. Keep it up.
Good job sir
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.
phenomenal - thank you for this
Thank you so so sooooooo much. It helped me alot
Thank you so much for your wonderful video
Thank you so much!!! 🧑🎓❤❤❤
Sanket Sir in the command prompt it's showing me could not open "protein.pdbqt" for reading.
Kindly help me Sir please.
thank you Sir for a beautiful explanation but how you are deleting the exsisting ligand
Thank you very much! It is really helpful 😊
Thanks a lot for all the details
How the config file was created ??
Make a text file by right click in the empty space on the folder ,choose text, open it then fill it by typing the Data ‘ rename the text file as config
thanks...was quite easy to understand..but getting error after entering docking command in cmd..kindly suggest...
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
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.
Explain please
Thank you -very informative video! could you please suggest how one can do these steps on mac as well? struggling with it for my project. I have prepared the ligand and protein and know how to use autodock/chimera but can't set up the code on command line mac
Thank you. It helped a lot.
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