AutoDock Tutorial - The best free software for molecular docking |Free Tutorial|
ฝัง
- เผยแพร่เมื่อ 28 ก.ย. 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 -
www.intechopen...
AutoDock - autodock.scripp...
MGL - mgltools.scripp...
Open Babel - sourceforge.ne...
View Another Tutorial for Making Educational Videos for free using Free software - OBS
• Record Educational Vid...
For Regular Videos , Please Subscribe My Channel - / @gatechemistry
You can Also Reach me on Platform :-
Unacademy - unacademy.com/...
Instagram - / reagentblues
Facebook - / reagentblues
Disclaimer
Copyright Disclaimer Under Section 107 of the Copyright Act 1976, allowance is made for "fair use" for purposes such as comment, news reporting, teaching, scholarship, and research. Fair use is a use permitted by copyright statute that might otherwise be infringing. Non-profit, educational or personal use tips the balance in favor of fair use.
The information provided on this channel is a public service with the understanding that Gate Chemistry makes no warranties, either expressed or implied, related to completeness, accuracy, reliability or suitability of the information. The channel disclaims liability for errors and omissions that may have crept in its content.
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?
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.
I cant se how the ligand was downloaded.can you please help me with that?
Thank youuuu. It's because of your video that I realized why I'm having several failures in the docking. QAQ
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?
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
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
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?
If possible can you make tutorial video on Mestronova. Stay safe sir❤
I have installed autodock and Vina but haven't get any shortcut on my desktop, what can I do?
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.
sir in docking my glg and dlg file is not generated in my system what we do
why did u not add polar H in your protein?
Isn't it important that grid should have a ligand covered along with peptide ??
Can you explain please how to use the results for? For example if the ligand activates the protein or inhibit the protein?
Please make video on molden software for molecular designing
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?
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
Great tutorial video, very helpful.... Keep making more videos on molecular docking
Do Anyone know the name of Ligand used in this docking?
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?
Can we save the receptor in pdbqt format just like the ligand? From save and write pdbqt
If there is more than 2-3 hetatoms... Then in this case do we need to delete all the hetatoms????
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?
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
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?
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?
Thank you so much. That was indeed informative and something new to learn.
Excellent teaching. Thank you boss!!
Best tutorial on autodock...thank you sir
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
Is there a way we can do covalent docking this way using this GUI ??
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 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.
Hi sir, I'm facing problem, after running autogrid and autodock, map file's are not generating, pls Help 🙏
ligand minimization ?
Sir I'm facing error after selecting grid>macromolecules>choose>select molecule and then error can you please help me 26:21
Thank a lot sir for making such an informative video.
if possible please make a tutorial using chimera software also
I'm unable to install mgl tools in windows7. Every time I'm trying to install mgl tools the program closes saying python molecule viewer not responding. Can anyone please help?
update your python
Thank you. Learnt something new.
@15:20 why do we need to remove heteroatoms
The website is down for a couple of months. Can someone please provide alternate links for download?
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
After download the PDB file of your receptor how do you visualize it?
does it need to download Rasmol or any other software?
it is indifferent visual tool, for example, discovey, studio, pymol, chimera, rasmol,
Very informative session........ thank you sir
Can't able to find autoGrid
Sir, can we use it for polymers as i am working on polymers and corrosion
no
Can I get all the links to download them
Sir when I run auto grid then the launch box appears and then dissappear suddenly. Even my file don't get save in map format as you have shown. Please suggest how to save map file
I have faced the same problem. I have window 7(32bit) on my laptop. plz, reply if u will get the solution. Thanks
please share more vdeos on cov-2
Sir,please tell softwares other than autodock and vina which can be used for protein ligand docking
Discover studio is another one. But I think we have to buy it.
It is used for visualization
swiss dock,paatch dock,par dock
very informative thank you very much
Thank you so much!
Thank you for this video
Nice and thanks
thank you
Thanks alot🥳
Can I install open babel and autodock vina in window 7 (32bit)??? Plz reply
Yaa you can install autodock vina but i don't know about open babel
@@samankhan2519 thank you for the information
pyrex is availble
Thank you sir 👍
Waiting for it
Wonderful
C:/Softwares/Workspace/autodock4.exe: FATAL ERROR: ERROR: 3411 records read in, but only dimensioned for 2048.
Change "MAX_RECORDS" in "constants.h".
C:/Softwares/Workspace/autodock4.exe: Unsuccessful Completion.
Sir you didn't mentioned which ligand you were using... Which made the tutorial useless for beginners like me. :'/
Exactly
One of the best tutorials indeed.Thank you!
This video was of grt help .Thanku so much sir . Would like to learn more about this .
Thank you for your excellent video and explanation .it helped my assignment .on ligand where to download was not told still managed to complete
Hi sir I followed your tutorial and got the results thank you so much for this session and please make more video like this 🙏
Can someone tell me where can I get the Autogrid.exe as I can’t jump running autodock without this file.
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.
Thanks for the content. Can you make a tutorial on protein - protein docking?
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?
@Gate Chemistry Hello Sir! My protein is Penicillin Binding Protein 2a (pbp2a), I deleted the watermolecules, added polar hydrogens and kollman charges. I did'nt delete the Heteroatoms in the protein which are the natural ligands ( Cadmium and Chloride ions ). It does'nt have an inhibitor too. But still the protein is not getting saved in AutoDock. What might be the problem Sir? Is there anything to do with the valency? It's showing that all atoms do not have an autodock_element field. And also coming to the ligand, it's a cadmium ion and I downloaded the 2D SDF format from Pubchem. I tried converting it from sdf - - MDL MOL format to pdb format as pdbqt option is not there for this ligand in Openbabel. But even the saved ligand pdb file is not being displayed when I am trying to select the ligand for optimization. I am a beginner in Bioinformatics. Please help me with this if you could. Thank you!
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...
An excellent video. cleared all my doubts about Autodock. Excellent Presentation. Thank You
sir, i cant able to zoom the molecule sir... will you please tell me how to zoom and zoom out.
Sir any free software for DFT calculations and put video on DFT calculations sir it's very useful to us
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?
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
Can someone help with this problem? pls swig/python detected a memory leak of type 'BHtree *', no destructor found.
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?
I am unable to save gpf file....it says you need to select macromolecule....even though I did select them
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...
Can anyone help me to get autodocking results
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.
what is the name of the ligand that you used?
Sir in my laptop .glg file is not creating after .gfg what should i do in that case
Sir I'm getting the problem on the Run when click it and follows all the step as you told but I didn't get the results as you Got
Please help sir
Do we need to Delete Water from Ligand??
please i cant found glg file , what's the problem ?
can u make a video on covalent docking using autodock4
I followed the same steps as u. Bt not able to opn softwares 😶
The grid option is not showing in mgl tools what to do now
how you prepare ligand file ??? this missed
Exceptionally great 🎉🎉🎉
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
How to download auto grid 4 sir
Will this software work on old processor
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...
Sir plz i want to learn autodock.
commenting for the algorithm
sir how to select ligand.