AutoDock Tutorial - The best free software for molecular docking |Free Tutorial|
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- Опубликовано: 22 авг 2024
- 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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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 :)
Hey.
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?
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!
please tell how to download the ligand?
@@epicakku5381 From pubchem
One of the best tutorials indeed.Thank you!
Hi sir I followed your tutorial and got the results thank you so much for this session and please make more video like this 🙏
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!
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.
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 👍
An excellent video. cleared all my doubts about Autodock. Excellent Presentation. Thank You
This video was of grt help .Thanku so much sir . Would like to learn more about this .
The best video on autodoc. A big thumbs up to you sir.
Exceptionally great 🎉🎉🎉
thank you so much sir, everything was so clear and perfect .thank you for making docking easier
Thank you Sir, for providing the best tutorial on Auto doc
Thank youuuu. It's because of your video that I realized why I'm having several failures in the docking. QAQ
I cant se how the ligand was downloaded.can you please help me with that?
As always explained in brief and clear .
Wow, extremely on point i literally had a protein from covid aswell gj dude
Thank you so much. It provides a clear understanding on autodock software
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.
Iam a research scholar (Biotech) really thank you❤❤....
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
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
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
Good explanation. Thankyou
It's really useful .
Best explanation .
Thank you soo much . Hope we will get more vedeos like this .
Sir you didn't mentioned which ligand you were using... Which made the tutorial useless for beginners like me. :'/
Best tutorial on autodock...thank you sir
This video is really good!! clear !!
Thanks for the content. Can you make a tutorial on protein - protein docking?
Very detailed and precise explanation... Ty so much
Great tutorial video, very helpful.... Keep making more videos on molecular docking
Excellent teaching. Thank you boss!!
Thank you for your excellent video and explanation .it helped my assignment .on ligand where to download was not told still managed to complete
Thank you so much. That was indeed informative and something new to learn.
Good explanation rather then other available video of autodock
I am using autodock 1.5.6
Waiting for more such video
sir plz use chimera software to remove C chain and prepare dock . It more easy
Very informative. Thanks for the video
Thank you . Elaborated very well.
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?
The best one thank you.
Very clearly explained... Thanks a lot😊
Thank a lot sir for making such an informative video.
If possible can you make tutorial video on Mestronova. Stay safe sir❤
Thank you. Learnt something new.
Thank you so much for this .....plz make more videos
Very informative session........ thank you sir
Very helpful.
Thank you very much sir.
Really good initiative
Very informative thank you for this session🤗
what is the name of the ligand that you used?
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...
Amazing 👌. Helped me generate results.
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?
Thanks. Nice tutorial.
I'm trying to follow your tutorial but you did not make your ligand available sir. How do I get the ligand you used?
My problem too,did you find the answer?
It is very helpful for me Bcz I am also same field like protein Ph. D 1st year student
Sir any free software for DFT calculations and put video on DFT calculations sir it's very useful to us
sir, i cant able to zoom the molecule sir... will you please tell me how to zoom and zoom out.
Please make video on molden software for molecular designing
Very well explained 👍
Thank you sir 😊 how I improve english sir
Practice everyday for 30 minutes without fail in whichever area you are weak in ND success will kiss your feet.
Thank you so much. It will be very useful
Thank you 🎉🎉
Thank you so much!
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.
Thank you for this video
Do we need to Delete Water from Ligand??
very informative thank you very much
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...
I have installed autodock and Vina but haven't get any shortcut on my desktop, what can I do?
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?
I have the same problem. Had you solved it? I would be very thankful for your help.
Nice and thanks
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.
Please make more videos on this topic..
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.
Very Nice. One question, How to know which Ligand is best? If I have 5 ligands, each one docked?
Plz make videos of this series 🙏🏻
sir in docking my glg and dlg file is not generated in my system what we do
Excellent!
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...
Good initiative sir...thank u
Great VDO. Request to make a video on Autodock VINA
Noted :)
Thank you very much.
Nice presentation.
Thanks alot sir
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?
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?
Sir in my laptop .glg file is not creating after .gfg what should i do in that case
when i run autogrid it starts but continues as such and never complete. what could be the problem?? neither map is generated
best tutorial ever .i am facing error during grid generation .I am unable to get map data .where will be problem exist ?
The grid option is not showing in mgl tools what to do now
I am unable to save gpf file....it says you need to select macromolecule....even though I did select them
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.
do you need to add hydrogens for electron microscopy structures? Or just x-ray structures?
Thanks alot🥳
Pls make a video on pharmacophore mapping and md..Thanks once again
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?
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?
Isn't it important that grid should have a ligand covered along with peptide ??
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?
can u make a video on covalent docking using autodock4
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?
Thank you soooooooooooooooooooooooo much