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

[@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

[@PatraGharaJhia]

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🙏

[@ayurvedasahitiprabha1116]

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

[@FESTIVEBLOGS]

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

[@ruhee4580]

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

[@dineshkrishnan4029]

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

[@user53f7f7ebs8w]

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

[@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

[@Alchemist_of_India]

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..

[@ruwanepa7443]

One of the best I have seen ! Thanks !

[@harshshukla1547]

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

[@hrithikroshanonly23]

Thank you ma'am this is very helpful for my project work

[@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.

[@indranisarkar3901]

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

[@organomed]

Glad it was helpful!

[@sharpgrin4345]

This is very educative, thanks so much

[@nishaapthoplagovender7047]

Great video!Thank you very 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

[@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.

[@adrianguinrizzo2735]

Awesome Tutorial! Thank you so much!

[@deshu7427]

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

[@organomed]

Thank you

[@smfarqadain7223]

Thank you for your perfect explanation

[@blackcat4714]

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

[@ayeshaansari9903]

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

[@quimicasuperior]

Thankss a lot! Simply beautiful

[@chemistry1452]

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

[@organomed]

Will try!

[@yogalakshmiperumal6030]

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

[@rimabd6096]

Thank you it was really helpful, I wish if you can made a video about re docking and how to get rmsd value for validation of program...I really need that...😢😢

[@يوونسعزاام]

thank you for complete explanation

[@alishamunwar7294]

Nice video sis.. so I made my ligand on avogadros. It is openable in auto dock vina and in discovery studio. I have clean protein as well. But when I try to interact them I fail to do so. I think I am missing some step. But not getting. Please help me

[@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....

[@Karmayogi-999]

It was amazing, thank you

[@priyanshugautam9892]

Maam I am getting problem at last when I reach at last step in command prompt it is written in error could not open "protien.pdbqt" for docking

[@priyanshugautam9892]

Please reply as soon as possible maam I need to sumbit my assignment on molecular docking tomorrow please 🙏

[@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.

[@nainadhiman2277]

Thankyou thankyou soooo much 🥺❤️❤️

[@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.

[@fun_zonealankrati]

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

[@nerminragab4522]

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

[@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.

[@fittycrame5752]

When we do docking, at the terminal, it said: "swig/python detected a memomry leak of type 'BHtree', no destructor found", and then my docking stopped half way. What does that mean? And what should i do? I'm usjng windows 11, 64-bit system.

[@hreethikarathod8057]

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

[@Mohamed.Aboulabed]

thanks alot you are very helpful

[@yaseenjanalchemist8026]

Really helpful much much better

[@বইয়েরআখড়া]

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

[@jaganathanr381]

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

[@SudhaMerla]

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?

[@simmim310]

I have many ligands and each ligand has different active site.. how should i define box parameters

[@duafatima6283]

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

[@ceren2977]

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

[@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

[@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.

[@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?

[@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

[@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.

[@NEHALRAMI-n3e]

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?

[@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

[@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

[@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

[@GeneMania2024]

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

[@darylfrancventura4552]

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

[@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?

[@lyradd]

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

[@mahenderthatikayala4415]

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

[@বইয়েরআখড়া]

you should make a video how we select the ligand

[@vaidehithakore798]

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

[@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

[@jyotiduhan220]

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

[@parthsharma6079]

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

[@fareehatahir1279]

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

[@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."

[@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.

[@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

[@poonamgupta9644]

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

[@faaizahbintmaqsood7000]

Simply for ligand protein docking is it mandatory to have Linux?? or Windows 11 is enough to perform??

[@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 🤗❤️

[@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

[@amnaaftab84]

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

[@sashanealand8315]

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

[@Pablo-tt5kv]

Hey there, how accurate is this software for determining the correct binding site for unknown compounds?

[@PatraGharaJhia]

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

[@eatwithblessed]

from where did you get docking folder? I couldn't find it in C

[@yaseenjanalchemist8026]

In autodock video you fisrt selected choose root here you selected detect root first why ? Please

[@saaptuvaruvom6589]

Pls make the pymol software and final result

[@Joshifamilydiaries]

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?

[@omprakashswami5301]

What are those files AD4 1_BOUND AND PARAMETERS?

[@kritikagaur2710]

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

[@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

[@chimkook9633]

Is it really necessary to add both charges in the protein?

[@hanaouahamada132]

thank you for this great job...but i did all steps I couldn't find the PDBQT in my docking file can you help please

[@chinoavoaja5420]

Please Ma'am, I can not find the 'confi' file on my laptop so what should I do?

[@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

[@indranisarkar3901]

very nice and helpful video. Can you please give LINK on minimization and dynamics run (GROMACS)?

[@organomed]

You cannot run gromacs on Windows. For that you need either Ubuntu or Linux system.

[@indranisarkar3901]

@@organomed I have installed in Linux . It would be helpful to see the steps and explanation of the output files

[@organomed]

Alright. I will try to make video as soon as I got some time.

[@dr.indranisarkar4671]

@@organomed can you show a demo on MD simulation of protein -ligand complex by NAMD in Windows10?

[@snigdhabonnechance7560]

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

[@sruthysaji3094]

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

[@Joshifamilydiaries]

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 .....

[@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?

[@sujankundu5918]

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

[@pushkarkumarray4567]

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