AutoDock VINA TUTORIAL || BEST FREE SOFTWARE FOR DOCKING || COMPLETE TUTORIAL

Hi Guys,
Welcome to OrganoMed!
In this tutorial, I had shown -
1. How to download and install Vina Software.
2. How to prepare protein using BIOVIA Discovery Studio.
3. How to predict the active site for docking.
4. How to run command prompt.
5. How to analyze docking score and results of vina.
Download Links-
Vina Software - vina.scripps.ed...
Biovia Discovery Studio - discover.3ds.c...
Configuration File Link - drive.google.c...
I hope after watching this video you all will be able to run autodock vina without facing any problem. If you like the video, then please comment down in the comment section.
Thanks for Watching!
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Email - [e-mail]
#autodockvina
#vinasoftware
#vinatutorial
#moleculardocking
#autodock
#discoverystudio
#organomed
#virtualscreeningusingautodockvina
#postdockinganalysis

[@novyherdiana9802]

thanks a lot, I've seen a lot of tutorials but only the tutorials from this video are very, very helpful. thank you

[@organomed]

Welcome!

[@peter_dockit]

This is the best video I have ever seen about docking

[@FESTIVEBLOGS]

You saved me after a long struggle I have finally learn to use it😊

[@ayurvedasahitiprabha1116]

Nice video and nice description of docking from scratch. Thank you a lot for making such tutorials.

[@user53f7f7ebs8w]

Thank you so much this was best one so far for vina. ❤

[@Solodiariesofpranjya]

Heartly Thank you.❤I really cannot do my work but by seeing ur videos i can do autodock upon Zika virus.Thank you so so much.Jay jagannath🙏

[@harshshukla1547]

Thanks mam I was able to do the docking with this video thanks a lot mam

[@ruhee4580]

This is one detailed tutorial ! thanks! and all the best for making new contents about the other tools too!

[@propharma1491]

Thks Organomed for such n elaborate n easy explanation of these software with its apt usage

[@organomed]

Glad it helped!

[@ebitimiomoni6521]

Thks alot, this video helped me when I was in school, 2021/2022.. Thank you

[@ruwanepa7443]

One of the best I have seen ! Thanks !

[@dineshkrishnan4029]

Thank you for your madam it was very helpful and it allowed me (a data analyst) to help my pharma girl molecules docked!

[@yes-jc8gb]

Yayy...worked for me smoothly.. I had failed many times before... And special thanks to introducing B. Discovery studio... Many many thanks... But I've few queries.. 1) B. Discovery studio or Pymol for visualization..(and why) 2) how to choose a protein... I am from chemistry background. I am planning to synthesis some novel compounds and study their anticancer property. But Choosing a protein is difficult for me. (This one is very urgent and very important for me) 3) can you please do a video on site specific docking 4) how to improve the dock score.. (this is also important).. Waiting eagerly for your reply thank you..

[@indranisarkar3901]

wonderful, it will help us a lot , specially the use of Discovery Studio . Thanks a lot

[@organomed]

Glad it was helpful!

[@ismaildin69]

You explained it in a very powerful way. To this day, I have not seen anyone like you explain docking with Protein ligand-binding sites as you explained. May ALLAH bless you.

[@yogalakshmiperumal6030]

Thankyou, helped a lot, I need for metal- organic ligand docking, kindly provide a video about it

[@nishaapthoplagovender7047]

Great video!Thank you very much

[@sharpgrin4345]

This is very educative, thanks so much

[@adrianguinrizzo2735]

Awesome Tutorial! Thank you so much!

[@adedayoayodeji938]

This is so comprehensive. Thanks for all the efforts put into this. I need to know how to create the configuration file. Thanks.

[@emmanuelonah4596]

Thanks a lot for this wonderful masterpiece. It was really very helpful

[@quimicasuperior]

Thankss a lot! Simply beautiful

[@smfarqadain7223]

Thank you for your perfect explanation

[@fun_zonealankrati]

If I don't know the zinc I'd for particular ligand, then how can I search?

[@deshu7427]

Thank you so very much for this video mam.. It is very helpful.

[@organomed]

Thank you

[@blackcat4714]

thank you so much your video is very helpful and easy to understand. you are the best thanks again

[@ravibalaskar3496]

In Autodock vina we get modes, binding affinity and RMSD values. Which mode, binding affinity value and RMSD value should I consider. I am using discovery visualizer for seeing interactions. Which ligand should we consider. What is the relation between modes in log file and ligand splited. Can you please make a detail video on this.

[@ayeshaansari9903]

thanks for creating such beneficial video, really helped me alot. 👍

[@caffeine-rd4vg]

hello mam, thank you so much for this video, it is really helpful but I have a doubt that how can we set GA runs in auto dock vina as I am not able to do that...

[@himanshikumar3579]

mam pls reply i also facing the same problem.

[@chemistry1452]

Hello It so clear and good demonstration Would please make a video of virtual screening through windows 10 in ubuntu

[@organomed]

Will try!

[@user-nv4nc9se3d]

thank you for complete explanation

[@NurAzizah-y2o]

what should i do if Parse error on line 1474 in file "CREB5_pdbqt.pdbqt": Unknown or inappropriate tag please help I stuck with it

[@poojazade7239]

I have one problem that my files of PDB that have converted in pdbqt in the software but in the pc. File that the haven't with the extension with pdbqt

[@quantumworld9487]

Hlo ma'am..the configuration link u have given in description box not opened it shows not found..plz replace it with new updated link plz....

[@priyankasingh1749]

It was amazing, thank you

[@divyakuratkar9655]

Split_exe not working shows the it is not recognised as an internal or external command

[@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?

[@darylfrancventura4552]

why did you choose ligand 1 instead of ligand 2 as the docking site?

[@jyotiduhan220]

Can u please tell me how we visualize whole ligand with protein structure actually my result showing result in parts I want whole

[@sruthysaji3094]

Why the structure of compound change after docking....? is it okey ?

[@sashanealand8315]

where is the docking folder where you pate the three vina things into?

[@duafatima6283]

Hi, thankS fro the video but why did you delete the chain B?

[@snigdhabonnechance7560]

Hii, I am not getting the out (out.pdbqt) file while doing the autodock vina commands..can anyone please help?

[@adrianguinrizzo2735]

Big question! Why do we add AD4 Type atoms, and calculate the Kollman and Gasteiger charges? It makes me curious, you do it but is not really explain.

[@nerminragab4522]

Thank you for your excellent explaination. Plz do you have any recommended publication with the same explained method to cite ?

[@nainadhiman2277]

Thankyou thankyou soooo much 🥺❤️❤️

[@jaganathanr381]

how can we fix the xyz distances for the protein which don't have a ligand???

[@rakhichaudhary9029]

Ma’am what if it is not opening in our system after doing every step

[@user-bn1il3sg9n]

mam please do a video how to select a ligand or docking

[@poonamgupta9644]

How do we know the Zinc ID of new compounds? Ligands>

[@gabrielbiancosilva5621]

Good morning, i have a doubt, do you know how the AutoDock make the Clustering process???? Which critery he uses so as to find and agroup similary poses??? Thanks for the attention.

[@parthsharma6079]

Hii ma'am can you please explain how can I install it in my ryzen software computer. After installation it's not opening 😢

[@gaurisharma5583]

My configuration file is not working. Help me please

[@yaseenjanalchemist8026]

Really helpful much much better

[@muhammadhassan4506]

thanks alot you are very helpful

[@sujankundu5918]

How you know that docking site will be in the site of ligand 1

[@unays]

Keep it up, you have been doing a great job. btw would you please, provide me a link to review articles for molecular docking. Your step would be appreciated.

[@adedayoayodeji938]

Hello. Can you help me on how to create the configuration file.

[@MountainStoner]

Mam it is showing as configuration file parse error : unknown option size X

[@hreethikarathod8057]

Thank you so much, can you please make a video on MD simulations

[@user-me4bi6kj8y]

Best explained. Appreciated. Could you plz provide the link to download "Biovia Discovery Studio" software? As link not working posted here. Is it free or liscence based software?

[@khushalkhan5238]

Hi, the Drive file isn't there kindly update on the issue

[@ceren2977]

Why do we add AD4 Type atoms, and calculate the Kollman and Gasteiger charges?

[@ferb.3045]

In terms of simplicity Vina is better than AutoDock, but the log from from AutoDock will bring more information. Is it correct to explore first with Vina and then select specific targets with AutoDock?

[@organomed]

It totally depends upon your choice and your research purpose.

[@krishnatrambadiya8093]

I didn’t found my protein in RCSB databank. But it is found in uniprot database. So kindly share the steps to retrive protein structure. Acetyl cholinesterase - Protein Meloidogyne incognita - organism

[@user-tc4dn9tg5y]

What are Gasteiger and Kollman charges? Where exactly are these charges being added in the protein? How can I determine the location of these charges in the protein?

[@kakalisarkar6757]

Thank you so much. It was really really helpful. I just have a single query. After preparing a protein in AutoDock tool (ADT), do we again need to go for energy minimization of that prepared protein before docking or we can simply proceed with the prepared protein exported from ADT for docking?

[@adedayoayodeji938]

Hi, please how do I go about the config file?

[@kushalsamanta1847]

Hey, how did you get the docking folder in C drive, where you pasted those three files? I don't get it. Once I install the msi file i didn't get any docking folder in c drive.

[@organomed]

For this issue I will suggest you to watch AutoDock video because in that video I had explained everything. For docking every folder must be present in a single drive.

[@organomed]

kzbin.info/www/bejne/mKqXoZRme6mnqs0

[@kushalsamanta1847]

@@organomed Thanks for your prompt response. I will check this video. Will definitely ask if I face any other issue. cheerio!

[@organomed]

@@kushalsamanta1847 welcome

[@meenublossom6860]

Hi.. Very nice explanation 👌👌but how wr would know that which chain i have to selectand which i have to delete. And also can we perform blind docking without selecting the ligand binding region. Thank you for the video ❤️

[@organomed]

To select or delete chains you nees to do literature search of the protein..and to the next question the answer is yes.

[@meenublossom6860]

@@organomed Thank you so much 🤗❤️

[@omprakashswami5301]

What are those files AD4 1_BOUND AND PARAMETERS?

[@ntejaswinisony4771]

Tq for the good lecture. But iam getting error in comman prompt. Like, Couldnot open my ligand , ( B-sitosterol) for reading. What should I do

[@vaidehithakore798]

Thank you, can you make a video for virtual docking using nPACT ligand Library?? It would be great. Thank you.

[@aichakerassa8857]

what is the meaning of "exhaustiveness"? is it always equal 8? ....thank you v much

[@organomed]

Exhaustiveness is the number of runs or u can say the thoroughness of search .By default it is set to 8.

[@organomed]

But you can change it

[@aichakerassa8857]

@@organomed thank u

[@Solodiariesofpranjya]

Can you please tell me how to write the result in thesis in about this work pls pls pls

[@amnaaftab84]

I downloaded autodock vina, but I don't have docking folder. What should I suppose to do now?

[@lyradd]

I wonder why was Chain B deleted? in 17:00 thank you!!

[@bajranglohan333]

good work

[@dadasaheb12377]

You have downloaded the autoduck 4.2 and auto dock vina both

[@mr.logan.5081]

Mam, in cmd prompt we type the comment but "configuration file phase error: unknown option centre _ x" showed . How to solve the problem? Pls help

[@appropiate]

When running autodock in command line, what spacing value is used? It is not specified in the config file. This parameter appears in the grid box window together with size and coordinates, and greatly influences the size of the grid box in autodock.

[@maikeru8458]

Where can I find the docking file in order to paste the vina?

[@whatsnew14]

Plz help me mujhy correct usage ki heading aur phr nech kafi Kuch likha hai but ye chart es tarha ni aarha sare steps follow liye still

[@chloeburbank4045]

thank you for this tutorial. using biovia was easier than using autodock to prepare the structures. however, i have a problem whenever i run vina. it can't seem to read my protein.pdbqt. i've followed all the steps in preparing the protein structure. please, can you help me? any advice would be greatly appreciated. thank you. for reference, here are the structures i am docking: protein = a3b4 nachr, ligand/peptide = mii conotoxin this is the error: "Detected 8 CPUs Reading input ... Error: could not open "protein.pdbqt" for reading."

[@user-bn1il3sg9n]

you should make a video how we select the ligand

[@kutubashraf9208]

hi can you kindly share the config file? thanks. very lucid explanation

[@hariprasadkulkarni5333]

Configuration file is not working. Can you reupload it?

[@kritikagaur2710]

i have an error while opening the conf.txt file in the command prompt , what should I do

[@purabsood8069]

Hello ma’am I’m getting a parse error on line 2 in file protein.pdbqt: unknown or inappropriate tag . Can you please help me resolving that

[@mahenderthatikayala4415]

How to done molecular docking group of lignads please make a video

[@ravitejaakubathini5954]

I followed this for blind docking for my assignment for 3v04 protein but I don't know the ligand name I did it I have to wait for my results

[@pushkarkumarray4567]

I have install the vina file but only showed vina file but don not show an autodock file. so please solve my problem

[@GeneMania2024]

Ma'am you haven't deleted hetero atoms during protein preparation.Doese it hamper really docking result?

[@almche8978]

Thank you. My labtop windows 10 but i cant open autodock after download it.

[@almche8978]

Type of system is 64 bit

[@navneetdhal5986]

Very helpful.

[@lifesciencedecoded]

Sir can we docked two target site for same disease by single ligand? Sir suppose x naam kaa ek ligand h jo A naam ke target site ko inhibit krra ho , phir suppose wahi x naam kaa ligand B naam ke target site ko inhibit krra ho, to sir kya hum ek saath A ligand ko dono target site(A and B) pe ek he saath docking kra skte h..... Multiple target site docking.... Sir plz doubt clear kar dijiye Agar kar sakte hain to kese ? Nahi kar sakte hain to kyu ni kr sakte?

[@RADHAKRISHNAN-mx2zn]

The command prompt runs only docking, How to run also vina_split madam?

[@organomed]

Watch the full tutorial ! I had shown how to run vina_split. After watching 32 min. you will find how to run vina_split . you need to enter vina_split.exe --input out.pdbqt and then press enter in cmd.

[@fareehatahir1279]

Hello, i have a question about number of torsions, is it ne6to kept the torsions less than 6 in vina?

[@adedayoayodeji938]

Thanks a lot for this great effort it's really helpful. How do I create the configuration file. Please I need help on that

[@akshaykt2499]

Can we get hydrogen bond distance from here?

[@nabeelbacker5870]

In my command prompt, it is showing:" vina.exe is not an external or internal command" and hence not running the program. what would be the possible reason, Does anyone know?

[@souvikbhandary9315]

Mam self docking means?