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

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

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4 жыл бұрын

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 -
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AutoDock - autodock.scripp...
MGL - mgltools.scripp...
Open Babel - sourceforge.ne...
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Пікірлер: 257

@anastasiyadudko1062 3 жыл бұрын

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 2 жыл бұрын

Hey.

@nihalkhan2541 2 жыл бұрын

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?

@ifeanyichukwueke9942 3 жыл бұрын

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 2 жыл бұрын

please tell how to download the ligand?

@devangmetaliya7 Жыл бұрын

@@epicakku5381 From pubchem

@simran1999 4 жыл бұрын

One of the best tutorials indeed.Thank you!

@dontshitamigo1260 10 ай бұрын

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 👍

@srilakshmivellanki4965 2 жыл бұрын

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.

@lifeinsequence Жыл бұрын

if you got Error of all atoms don't have autodock element field while saving it in pdbqt format then after removing water--> adding H --> go to edit--> atom --> assign AD4 type then last step add Kolman charge and save it in pdbqt format.

@TheAbzaby 3 жыл бұрын

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

@vijays4092 4 жыл бұрын

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

@krishnamaskara56 4 жыл бұрын

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

@tinacole1450 2 жыл бұрын

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!

@shail2269 Жыл бұрын

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

@ronniegamerz8568 2 жыл бұрын

for getting ligand on the dock u done even need pymol u can just click on all molecule -- add molecule on the dock and aadd the file

@sandipbarman9134 2 жыл бұрын

Please help What is the basic system requirements for the program run? I'm a fresh student of don't have any idea about computer

@10tus61 2 жыл бұрын

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

@selviapriliana9477 2 ай бұрын

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?

@harshathanreddy717 3 жыл бұрын

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

@joaopadua7134 2 жыл бұрын

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

@princeshukla2117 4 жыл бұрын

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

@DEEPAKCHAUHAN-tk8cb 4 жыл бұрын

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

@user-lw4gj9dy2t Жыл бұрын

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

@cjaytv5664 4 жыл бұрын

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

@alphaViolinist 2 жыл бұрын

Iam a research scholar (Biotech) really thank you❤❤....

@sandipbarman9134 2 жыл бұрын

Please help What is the basic system requirements for the program run? I'm a fresh student of don't have any idea about computer

@Nabarun_Dawn Жыл бұрын

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.

@SamriddhiJaswani Жыл бұрын

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?

@jayashreeprabhakaran227 4 жыл бұрын

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

@jaydeepmokariya823 4 жыл бұрын

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 4 жыл бұрын

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

@lotfy745 2 жыл бұрын

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.

@shikhalalwani7240 4 жыл бұрын

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?

@charlesarineitwe505 2 жыл бұрын

thank you for this elaborate video, managed to follow it well. I however, am not getting successful docking results, i keep getting this, any help will be appreciated. Thank you C:/Program Files (x86)/MGLTools-1.5.6/autogrid4.exe: Sorry, I can't find or open Grid Parameter File "C:/Program" C:/Program Files (x86)/MGLTools-1.5.6/autogrid4.exe: Unsuccessful Completion. AutoDock needs the extension of the docking parameter file to be ".dpf" C:/Program Files (x86)/MGLTools-1.5.6/autodock4.exe: Unsuccessful Completion.

@samaptimondal8008 11 ай бұрын

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?

@samanthagottschalk7285 4 жыл бұрын

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...

@mohammadovaisdar6626 9 ай бұрын

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?

@lateef230 2 жыл бұрын

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

@rakshapandit6139 3 жыл бұрын

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

@gpavankumar1974 4 жыл бұрын

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

@niveditabhardwaj6733 4 жыл бұрын

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?

@nikhilsaripalli4085 5 ай бұрын

Good explanation. Thankyou

@chemistryalive5851 Жыл бұрын

As always explained in brief and clear .

@dharshudharbar 23 күн бұрын

sir, i cant able to zoom the molecule sir... will you please tell me how to zoom and zoom out.

@kirtisharma8609 3 жыл бұрын

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

@devyandas8315 4 жыл бұрын

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

@MMI_Updates Жыл бұрын

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

@sayansamanta3775 Жыл бұрын

what is the name of the ligand that you used?

@aneesamuzaffar4450 Жыл бұрын

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

@MsMohanakrishna 4 жыл бұрын

best tutorial ever .i am facing error during grid generation .I am unable to get map data .where will be problem exist ?

@satheeshk007 4 жыл бұрын

Sir any free software for DFT calculations and put video on DFT calculations sir it's very useful to us

@EM-bw7fs 2 жыл бұрын

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?

@HominidPetro Жыл бұрын

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

@hareembintihassan9885 4 жыл бұрын

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...

@babitapruseth2707 4 жыл бұрын

Best tutorial on autodock...thank you sir

@Leader_0_1 4 жыл бұрын

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

@devanshigupta5390 2 жыл бұрын

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"

@dhairysharma5171 3 жыл бұрын

Very detailed and precise explanation... Ty so much

@alekyaallu8801 2 жыл бұрын

Isn't it important that grid should have a ligand covered along with peptide ??

@shrutibhatt590 3 жыл бұрын

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

@knowledgeseeker9757 Жыл бұрын

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

@sambitpradhan6292 4 жыл бұрын

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...

@diptendusarkar1912 3 жыл бұрын

after running your protocol, I am not getting any result, not showing any thing, what could be possible reason? kindly help me out.

@shaguftaansari6780 3 жыл бұрын

Could you please explain about the ligand part too..how to select and prepare ligand ...its a humble request......and it will be so helpful in learning too...Thankyou.

@azraelwai Ай бұрын

Sir you didn't mentioned which ligand you were using... Which made the tutorial useless for beginners like me. :'/

@peterarome-nj7ll 2 ай бұрын

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?

@christotimothy8730 2 жыл бұрын

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?

@biswajitbiswas2960 4 жыл бұрын

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?

@sanatabassum4043 2 жыл бұрын

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 ????

@nilimadas3466 4 жыл бұрын

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

@saimaejaz246 Жыл бұрын

hello, tutorial was great. I am following it for docking. but at the last step i get the error Opening Grid Map Dimensions file: cRaf.maps.fld Grid Point Spacing = 0.000 Angstroms Even Number of User-specified Grid Points = 0 x-points 0 y-points 0 z-points E:/MGLTools-1.5.7/Workspace/autodock4.exe: FATAL ERROR: insufficient grid points. E:/MGLTools-1.5.7/Workspace/autodock4.exe: Unsuccessful Completion. However, i have selected grid spacing 0.2. But i don''t know why it is showing grid spacing as zero in dpf file. i have tried several times. can you help me.

@tamilidiotbox9071 Жыл бұрын

Bro really good career in computational chemistry? Please say that how many companies are available in the field ? Please any one say very useful for my future career

@shannenmiller5758 4 жыл бұрын

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?

@microsoftsimba6990 3 жыл бұрын

Do we need to Delete Water from Ligand??

@TheMushtaqkakar 2 жыл бұрын

Hello! Many Thanks for such easy to use video on autodock...could please share a link for video on autodock vina.... if there is any

@joshuasaucedal7006 Жыл бұрын

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

@pratikkatare2468 3 жыл бұрын

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

@PriyaDharshini-sq2mb 2 жыл бұрын

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?

@souravmajumdar128 3 жыл бұрын

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

@sravanipolavarapu9865 3 жыл бұрын

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

@ashmithaelangovan6141 3 жыл бұрын

Hello Sir...I followed all the steps and procedure but during running autogrid i get error notification i have repeated it several times but still i get error what is the procedure to detect and rectify the error Sir..Can you please help me to solve this issue

@yuvrajk.c.9665 3 жыл бұрын

when i run autogrid it starts but continues as such and never complete. what could be the problem?? neither map is generated

@kiyimbakennedy27793 9 ай бұрын

Very informative. Thanks for the video

@abhijeetaher4701 3 жыл бұрын

Sir, will you please make video on ligand ligand docking, is it possible?

@okayworld1208 3 жыл бұрын

Excellent teaching. Thank you boss!!

@aditideshmukh1878 Жыл бұрын

Sir I'm facing error after selecting grid>macromolecules>choose>select molecule and then error can you please help me 26:21

@souravsutradhar6602 4 жыл бұрын

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

@navamallikadutta7043 4 жыл бұрын

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?

@saswatiroy3700 Жыл бұрын

Please make video on molden software for molecular designing

@NamrathaUllal1697 4 жыл бұрын

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

@significantmatters8740 3 жыл бұрын

sir, do we need to check for missing atoms and repair them?

@MalithArambage 11 ай бұрын

This video is really good!! clear !!

@lifesciencedecoded 3 жыл бұрын

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?

@yogi5752 3 жыл бұрын

As far as I know you should go for site-specific docking. So first you dock X ligand with A site . Get the results. Then again dock X with site b separately to get the results. So you should be careful while preparing the Grid. I think it solves your problem

@Shubhamkumarzx 2 жыл бұрын

Please specify a receptor before trying to write a grid dimension file is popping up on screen when I clicked on output grid dimension file. How to do grid generation step to proceed ahead?

@academictipsblog 2 жыл бұрын

I have the same problem. Had you solved it? I would be very thankful for your help.

@mukhtarahmad6309 Жыл бұрын

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 ...

@anupamaroy8893 4 жыл бұрын

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

@divyaprasadsinghdev274 2 жыл бұрын

How can I make a ligand? Are there any free softwares or can I get chemsketch or chemdraw for free? Cause I don't think I can afford it... - am a student pursuing Btech in Biotechnology

@amnashafqat2799 5 ай бұрын

The best one thank you.

@pratyushmohapatra8184 3 жыл бұрын

The video is really nice. You explained and showed everything very nicely but the link to install the application is showing some problems. could you send the link to install the application again or do some changes?

@rousunarakhatun1153 4 жыл бұрын

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

@lifesciencedecoded 3 жыл бұрын

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

@abhinavgupta1089 2 жыл бұрын

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?

@joydeepmahata5579 6 ай бұрын

why did u not add polar H in your protein?

@keyajoshi3965 2 жыл бұрын

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

@TeenaATeenaAntho 3 жыл бұрын

Very clearly explained... Thanks a lot😊

@pooranirajendran5414 4 жыл бұрын

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.