Autodock Vina Tutorial - Molecular Docking

[@manaljain9525]

Heartful of thanks Sir....this really helped me to perform docking for the first time, thanks a lot💖

[@27b11]

Thanks very much! This video help my life.

[@FarhanHaqj]

Good to know

[@10tus61]

Thanks for sharing this! It's really hard to just read manuals in the internet so this is really helpful to me. 😍

[@munshot]

Thank you sooooo much!!!

[@FarhanHaqj]

Pleasure

[@JuliusCeazarLumbang]

thanks my friend

[@jlscrub]

This was a nice tutorial but it does not show how the final drug docked onto the protein structure.

[@lifesciencedecoded]

Sir jese hum docking karte time receptor protein kaa interaction karte hain , us time receptor protein kaa water remove karte hain, or ligand kaa interaction karte hain, but natural condition main recepror protein main water rahega, phir interaction kese hoga..... Sir plz doubt clear kar dijiye .... Usually water active site ko distort krta h interaction ke time, tbhi hum water molecules ko remove karte hain , but jab hum koi medicine/ligand create kar lenge to wo to phir body ke inside receptor protein main water hone se interaction hi nahi hone dega natural condition main..... Plz clear the doubt of my question sir .....

[@kimjunha1575]

Thanks for nice video!

[@duafatima6283]

Hi,Thanks for the video but I'm having an error as '--receptor' is not recognized as an internal or external command, operable program or batch file', can you please guide me what's wrong?

[@aritromaity1022]

thank u very much for such an amazing video......please tell me how did u create the output.pdbqt file and when

[@sandhyadaroji3531]

Hello, great vid. It would be really great if you could tell me how to do this,can I insert a substrate and see how it binds?

[@sanehobbies2385]

sir, what to do when we don't have the x,y,z coordinates of the binding site?

[@SufyanKhan-qv4js]

Hi very informative tutorial on AutoDock Vina but I have a question which is that what about if we don't know about the ligand binding site of our protein so how can we set the grid?

[@shanavazh2341]

Sir please upload metal based ligand docking study - autodock vina Thank you

[@praveenjkpg]

based on your installation process i did not found the scripps research institute location

[@ArnavPadhi]

please send the link to download the autodoc software

[@ananyapandey2577]

Thank you so much sir for this video...but am facing issue its written here parse error on line 1 in file ligand.pdbqt unknown or inappropriate tag

[@mohamedsase7250]

Thank you dr for great video I want to ask if i can download it for 64 bit windows or not and if there is any away for do it ? Thank you alot

[@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?

[@amitaverma4928]

You are awesome. Do u know about free software of MD simulation? Please let me know. Thanks

[@FarhanHaqj]

Gromacs Namd

[@ashmithaelangovan6141]

Hi...Thank you so much..I had lot of confusions in running autodock vina now im clear with the concept of using autodock vina Thank you again...😊

[@FarhanHaqj]

Happy to know this

[@tiff2072]

Hello sir, i have seen people adding hydrogens during the docking process as you did. May I know what is the reason behind this?

[@benmiloudloubna2062]

????????

[@RajeshKumar-fr7rx]

Energy range and exhaustiveness tell me waiting for this ... Before all method finished .., still wait this part

[@iqrahasan9114]

Can you please tell me how to make configuration file please..

[@zainabahsan2369]

Sir should we download ligand in 2D or 3D form?

[@FarhanHaqj]

Its upto you !

[@zainabahsan2369]

@@FarhanHaqj sir if a protein's active domain is between 600 to 700, but my comes less than 500.what could be the reason?

[@muqadasazahid1003]

my downloaded file is not executable kindly help... i have tried many times

[@shahbazghalib8954]

From where the log.txt file come we have to create it by ourself

[@santiagobolivaravila9469]

Hi, I do all the steps as you show in the tutorial, but when I run vina, I get this message: Command line parse error: adjacent parameter is empty in 'receptor'

[@FarhanHaqj]

Please follow it carefully. Maybe you are missing some file.

[@manaljain9525]

When you download a pdb file from pdb site, do not change its name, let it be the 4character name (like 3hf1), you can chage the name to target or receptor or any other name while saving it as pdbqt file through autodock, this name will be as it is in config file and cmd.....may this solve your problem👍🏻

[@hafsahmureed873]

Hello, I have followed the same process, but when I am running Command prompt I got the following error: "Configuration file parse error: " unknown option centre_x" . kindly suggest solution.

[@FarhanHaqj]

Make sure your pdbqt file is written correctly before running it.

[@RajeshKumar-fr7rx]

Sir how save config file 🙄🙄 Pls tell me (Any one reply)

[@Shadow-bx8ri]

Easy, clean and well explained. Heartiest thanks to you, sir.

[@sunilsethi3465]

Thank u sir But am having an issues while doing this. Can u Plz help me out... While writing the command for Conf.txt file.. It is showing error " couldn't open "conf.txt" for reading. What to do next....?

[@FarhanHaqj]

Please check the extension of the file. Possibly it would be config.txt.txt, change it to config.txt and try again.

[@sunilsethi3465]

@@FarhanHaqj Thank you sir. I will check.

[@prachitadessai1533]

can somebody help me?? im unable to download the autodock vina app using the above link.... please can anybody help

[@noamarson6345]

Neither can I !

[@great2395]

how to create the log text?

[@arshiyababbar8577]

how to know which ligand interacts with the protein?

[@FarhanHaqj]

Thats what you have to search from the previous studies to choose the best possible ligand(molecule) for your desired protein.

[@arshiyababbar8577]

@@FarhanHaqj There is not a particular drug for that for that particular organism

[@appropiate]

I have done as instructed and get the following error: Parse error on line 2 in file "ligand.pdbqt": Unknown or inappropriate tag the line 2 in ligand.pdbqt file is: HETATM 1 F UNK 0 11.717 -3.856 0.000 0.00 0.00 -0.179 F Any help appreciated, thanks!