AutoDock Tutorial - The best free software for molecular docking |Free Tutorial|

Learn how to use AutoDock software which is used for Molecular Docking
This a tutorial for basic understanding how to run a docking simulation.
Principles of Molecular Docking -
www.intechopen.com/books/drug...
AutoDock - autodock.scripps.edu/downloads...
MGL - mgltools.scripps.edu/downloads
Open Babel - sourceforge.net/projects/open...
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[@simran1999]

One of the best tutorials indeed.Thank you!

[@anastasiyadudko1062]

I want to thank you. Your video provided me with a quite clear and good understanding of the Autodock soft. Good job :) P.s. I also want to send " Hello" from young Belarusian biochemists to all people, who are engaged by modeling, docking, and science as well :)

[@nihalkhan2541]

Hey.

[@nihalkhan2541]

I am a very beginner in this field of molecular docking. I have a query that the way we have Protein data bank, do we have compound data bank? Can we do docking on compounds as well?

[@tinacole1450]

Thank you so much. I could not use Mcule for an assignment b/c I needed to wait for a confirmation email that never came. This has a little bit more functionality but it has helped me greatly! Thanks!

[@vijays4092]

Hi sir I followed your tutorial and got the results thank you so much for this session and please make more video like this 🙏

[@harshathanreddy717]

thank you so much sir, everything was so clear and perfect .thank you for making docking easier

[@shannenmiller5758]

Hi. Thank you for the tutorial, it was really useful. I try to set GLN189 as a flexible residue and run the docking but it is not working. Do you know if there is another specific file .DAT or any other file I should have in my directory?

[@dontshitamigo1260]

Yes this video was very helpful 😅 I was so scold by my guid for not learning within the time frame and then thru ur video I was able to get a good grasp on it at short time 👍

[@DEEPAKCHAUHAN-tk8cb]

Thank you Sir, for providing the best tutorial on Auto doc

[@TheAbzaby]

An excellent video. cleared all my doubts about Autodock. Excellent Presentation. Thank You

[@krishnamaskara56]

This video was of grt help .Thanku so much sir . Would like to learn more about this .

[@hareembintihassan9885]

Sir , can u plz help me out in knowing how to add new atom parameters for metal ions in Autodock as I am supposed to dock some metal complexes as ligands whose parameters are not present in default library...

[@NamrathaUllal1697]

Thank you so much. That was indeed informative and something new to learn.

[@chemistryalive5851]

As always explained in brief and clear .

[@samanthagottschalk7285]

Does anyone know if there is a way to do docking if your ligand should be covalently attached to one of the amino acids with autodock vina? I have seen a lot of places directing to the same paper but even then I still can't figure it out...

[@cjaytv5664]

I cant se how the ligand was downloaded.can you please help me with that?

[@parvejkhanpk]

Thank you. Learnt something new.

[@okayworld1208]

Excellent teaching. Thank you boss!!

[@shail2269]

The best video on autodoc. A big thumbs up to you sir.

[@bidhanchandramalakar2219]

Thank you . Elaborated very well.

[@shikhalalwani7240]

I am unable to download protein sequence file in pdb format... it is being downloaded in gaussian... Can u please suggest me what can I do to avoid it?

[@devyandas8315]

Thanks for the content. Can you make a tutorial on protein - protein docking?

[@user-lw4gj9dy2t]

Thank you so much. It provides a clear understanding on autodock software

[@niveditabhardwaj6733]

This video is really helpfull...can you tell me to excute docking you have choosen option from "docking" instead of using "command prompt" and making a separate config file..so is the output results is same from both ways?

[@rakshapandit6139]

Great tutorial video, very helpful.... Keep making more videos on molecular docking

[@dhairysharma5171]

Very detailed and precise explanation... Ty so much

[@navamallikadutta7043]

M not being able to load the Macromolecule for docking after creating the grid for both the protein and ligand. What could be the reason?

[@imensouid7743]

Dear. Thank you very much for this interesting video too clear But I find a problem when using the Run AutoGrid that's I cannot find Program Pathname, Parameter Filename and Log Filename. I will be grateful if you tell me from where can I select them.

[@pooranirajendran5414]

Thank U very much sir.... I have tried this with my Metal docking with my protein. When I try to run autogrid. This shows an error that can't find or open the receptor PDBQT file. Can you help me to recover this error sir.

[@manju8109]

Thank a lot sir for making such an informative video.

[@samaptimondal8008]

Hello sir, I am docking for silver nanoclusters (instead of protein) with ligand but the Autogrid run is showing unsuccessful due to unknown receptor type. What should I do for that?

[@abhinavgupta1089]

Hi, The tutorial was nice. Can you also help with the docking if we have two active sites of a homodimer with the same ligand?

[@jayashreeprabhakaran227]

Thank you for your excellent video and explanation .it helped my assignment .on ligand where to download was not told still managed to complete

[@EM-bw7fs]

Thank you verry much. Can you help me please. Why autodock vina does not generate the dlg files foor acids such as coumaric, caffeic, gallic ...etc?

[@aneesamuzaffar4450]

How should I convert affinity obtained into binding constant (kD)? At what temperature does Autodocvina runs?

[@babitapruseth2707]

Best tutorial on autodock...thank you sir

[@loveedetmendie]

After running autogrid it said successful, then I moved to run the autodock it says "I can't find or open ligand", please how do I rectify this

[@10tus61]

Thank youuuu. It's because of your video that I realized why I'm having several failures in the docking. QAQ

[@nickalbbar]

Best tutorial. Thank You. I've run into a problem though. When i'm going to run the AutoDock i get the following error "Autodock needs the extension of the docking parameter file to be dpf" but my file is already in the dpf format. Can you help or someone in the comments ?

[@TeenaATeenaAntho]

Very clearly explained... Thanks a lot😊

[@pavithrar3384]

Very informative thank you for this session🤗

[@princeshukla2117]

It's really useful . Best explanation . Thank you soo much . Hope we will get more vedeos like this .

[@lateef230]

I follow all instructions regarding installing and preferences files.it’s gone koi till I was preparing ligand to be saved in workplace folder as preferences path.software then refuse to save ligand as pdbqt in this folder and causing that I have not anther to do that and should contact the administrator and suggest another pathway instead. Please help me to solve that thanks in advance

[@peterarome-nj7ll]

The autodock Vina and mgl tools I downloaded didn't come a folder as yours and hence, I could not locate the autodock Vina.exe and autogrid.exe. can anyone help me?

[@selviapriliana9477]

thank you so much for your expalnation sir, i got the obstacle in add cofactor to reseptor, would you mind to help me for solve this problem?

[@PriyaDharshini-sq2mb]

sir i have a doubt. why arent maps generating for me? I did get it as successful after running the autogrid, but except the gpf and glg file, i did not get any maps?

[@pratikpatel7198]

Thank you so much. It will be very useful

[@manju8109]

sir after clicking the launch button in run Autogrid....the map files are not generating even having all files in the same location..plz suggest.

[@sanatabassum4043]

Hello sir it’s very informative video... i have a question that can we dock multiple ligands at one time with single protein with autodock4 ????

[@christotimothy8730]

why does it show all atoms do not have an autodock_element field .pdbqt file is not generating when i try saving it as pdbqt?

[@MMI_Updates]

I have installed autodock and Vina but haven't get any shortcut on my desktop, what can I do?

[@Leader_0_1]

Can you explain please how to use the results for? For example if the ligand activates the protein or inhibit the protein?

[@joaopadua7134]

Wow, extremely on point i literally had a protein from covid aswell gj dude

[@devanshigupta5390]

Hello sir my map files have not created. Can you tell me where I can be wrong? Opening glg file with notepad error is showing "can't find or open receptor PDBQT file"

[@mukhtarahmad6309]

Do all your downloads come in your "workspace" folder .. if so how have you generated it within" Autodock Tools" folder ? Please help me in this ...

[@biswajitbiswas2960]

Very informative! One single problem, I have a Mac! and the installation process seems very different! Otherwise I guess the workflow will be the same right?

[@nilimadas3466]

my protein doesnot contain cl atom which is there in the ligand and maps are generated for all atoms in the protein. while autodocking its showing the error: I'm sorry; I can't find or open "5nm2.Cl.map" the atoms in protein are : A C H HD N OA SA and atoms in ligand are:A Cl OA N pls tell how remove the error

[@neerajkumarsah2940]

I couldn't download the mgltool exe file. while downloading some error is occurring. I don't know why. is there any exe file of mgltool available for win 64 bit?

[@lotfy745]

good day, at first I thank you very much, I followed the steps but when I opend the ligand on autoduck it appears away from the macromolecule, not in it, so, how can I solve this problem.

[@ifeanyichukwueke9942]

I was following the tutorial until you jumped to the ligand selection. I wished you had specified where you got the ligand and showed us how you prepared the ligand (I know the preparation is the same as the target). Other than that, nice video!

[@epicakku5381]

please tell how to download the ligand?

[@devangmetaliya7]

@@epicakku5381 From pubchem

[@HominidPetro]

do you need to add hydrogens for electron microscopy structures? Or just x-ray structures?

[@MalithArambage]

This video is really good!! clear !!

[@kirtisharma8609]

I am getting some error while drawing grid box: >>> adding gasteiger charges to protein UNL1 not in qkollua; charges set to 0.0 Exception in Tkinter callback Traceback (most recent call last): Something of this sort please help

[@srilakshmivellanki4965]

Its really informative and very helpful. Great video but I would like to give one suggestion, don't get confused in the middle and don't rush. It's confusing the viewers as well.

[@asingh56]

Thank you so much for this .....plz make more videos

[@jatinkashyap1491]

Thanks. Nice tutorial.

[@sambitpradhan6292]

I'm facing problem in the time grid... Not able to save the gile as pdbqt... After clicking grid, then select macro molecule, aftr selecting its show some problem...

[@mohammadovaisdar6626]

Very informative. I have one query 47:11 ,the RMSD is more than 3 and as far i know i should be less than 2. so what is the reason for high RMSD and how can we reduce the RMSD?

[@prajwaldhokne6470]

Very helpful. Thank you very much sir.

[@kiyimbakennedy27793]

Very informative. Thanks for the video

[@pratibhasrivastava7508]

very informative thank you very much

[@sravanipolavarapu9865]

Can we save the receptor in pdbqt format just like the ligand? From save and write pdbqt

[@dr.neetaazad3082]

Thank you for this video

[@pedroaugustolemossantana259]

Thank you so much!

[@AhmedAli-vq7oy]

Thank you very much.

[@anupamaroy8893]

If there is more than 2-3 hetatoms... Then in this case do we need to delete all the hetatoms????

[@lifesciencedecoded]

Sir mere binding energy pyrx virtual tool se -12.2kcal/mol aare h , but DSV se result analyse krne m unfavourable bumps, alkyl, vandevall interaction aese show hore hain.... To sir kya ye galat hai

[@joshuasaucedal7006]

Can someone help with this problem? pls swig/python detected a memory leak of type 'BHtree *', no destructor found.

[@knowledgeseeker9757]

Hello sir why I get different docking score with autodock vina(with same protein and same ligand)?

[@nikitaabramenko4490]

Hi, can i ask you, which ligand is used in video? Thx!

[@Tekofilic]

Can someone tell me where can I get the Autogrid.exe as I can’t jump running autodock without this file.

[@pratikkatare2468]

Sir in my laptop .glg file is not creating after .gfg what should i do in that case

[@rousunarakhatun1153]

It is very helpful for me Bcz I am also same field like protein Ph. D 1st year student

[@Nabarun_Dawn]

I am facing this problem while docking after grid preparation. It is showing: C:/AutoDock/autodock4.exe: FATAL ERROR: ERROR: 2393 records read in, but only dimensioned for 2048. Change "MAX_RECORDS" in "constants.h". C:/AutoDock/autodock4.exe: Unsuccessful Completion. Please help, Sir.

[@nikhilsaripalli4085]

Good explanation. Thankyou

[@jaydeepmokariya823]

Good explanation rather then other available video of autodock I am using autodock 1.5.6 Waiting for more such video

[@dr.r.b.tripathi3733]

sir plz use chimera software to remove C chain and prepare dock . It more easy

[@anilkanda162]

Really good initiative

[@bikashjyotigohain7984]

Good initiative sir...thank u

[@amnashafqat2799]

The best one thank you.

[@jyotiyadav683]

Very informative session........ thank you sir

[@sudiptadash5122]

Is there a way we can do covalent docking this way using this GUI ??

[@souravmajumdar128]

great informative video sir. while running autodock i get an error error in readmap, too few values read in check grid map a . pleases someone provide me the solution

[@DivineDarshan_YT]

sir in docking my glg and dlg file is not generated in my system what we do

[@jatinkashyap1491]

AutoGrid works fine. But on AutoDock it shows following error "C:/Users/Public/Autodock/workspace/autodock4.exe: I'm sorry; I can't find or open "6lu7.pdbqt.P.map". I am getting every other file generated except the above one during AutoGrid in my environment/workspace folder. Anybody else facing it?

[@shrutibhatt590]

I am unable to save gpf file....it says you need to select macromolecule....even though I did select them

[@gpavankumar1974]

Very Nice. One question, How to know which Ligand is best? If I have 5 ligands, each one docked?

[@sayansamanta3775]

what is the name of the ligand that you used?

[@souravsutradhar6602]

If possible can you make tutorial video on Mestronova. Stay safe sir❤

[@keyajoshi3965]

How do you extract the final docked pose with your receptor??

[@SamriddhiJaswani]

I've followed your tutorial step by step but am unable to run AutoDock and getting an error that says: I'm s orry; I can't find or open "2f9a.F.map" Can you please tell how to solve this?

[@scienceclassesbykeshav7036]

Amazing 👌. Helped me generate results.