AutoDock Tutorial || Molecular Docking || Best and Easy Way ||
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- เผยแพร่เมื่อ 11 ก.ย. 2024
- Hi Everyone!
Welcome to OrganoMed.
In this Video, I had demonstrated how to download, install and run AutoDock as it is one among the best software available for Molecular Docking.
Link of all the softwares used in molecular docking -
Python - www.python.org/
MGL Tools - mgltools.scripp...
AutuDock - autodock.scripp...
Open Babel - sourceforge.ne...
I hope after watching this video everyone will be able to run AutoDock smoothly. Watch this video till end!
If you like this video please share it and subscribe OrganoMed.
Thank You.
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#moleculardocking
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#docking
#blinddocking
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OMG thank you so much this has solve the problems I´ve been having for a month!!!!
you are amazing
I am really happy to listen that this video is solving your problems.
@@organomed you are also a great teacher so that helps too
@@ferb.3045 Thanks
Finally, I understand Autodock after this tutorial..... Before that, I have tried at least 5 different tutorials on youtube. YOU ARE AWESOME
Thank you
Can u help me please
Thank you so much for making this video
I am watching it after 3 years and it is very helpful for me
UPDATED comment: Your video has it so easy. I struggled for months to find a video like this! Thank you for the help and for this great video! I would share this video! Thanks xx
Glad to hear it!
This beautiful and smart lady has helped me so much. God bless you
Glad it helped you!
This is the new aspirant of docking learner sooo I hope that I’ll learn more from you inshallah
Thanks a ton. I was really struggling with the last step. Excellent way to clear for someone new in this field.
Pleasure to hear it!
I had been trying to run docking but there was always some problem, that i couldn't get my results. Thanks to you i finally got my results. much love and thanks🥰
I am now face this same problem......I can not run the docking.......kindly guide me
This is the best video have ever seen about docking
The only tutorial that proved helpful! TYSM
Glad it helped you!
You are just growing amazing day by day❤❤.. best wishes...
Thank you so much 😀
Thank you so much for clearing the concept. I have watched so many videos but I got the final result of docking with the help of this video only.
Its really well detailed and clarified regarding steps to steps of auto docking right from the downloading the softwares to finally building a molecule.
😮❤❤❤❤
Thanku so much for this video ..I was having lot of problems earlier ..but the way u mentioned every details so nicely .. thanks
My pleasure!
Thank you for making this tutorial, I've completed all the steps and get the results! Thank you so much 💛
Hello, when i click to Run, i have an error message like the grid can't find my folder docking, can u help me please
Thank you very much, i learned a lot of very important things. I visualized all your Videos, which I left a like for all the videos. Thank you and a thousand thanks.
Glad it is helpful! Happy to hear it.
Fantastic video... no words tq..
I'm happy to come across this tutorial it's a blessing.
You explained each and every step so well, it cleared most of my doubts regarding autodock
Thank you for that.😇
Thank you so much for such a great video on molecular docking. Each step is explained so well and it has become so easy to do. Once again thank you 😇
thank you so much, very helpful much appreciated.
Thank you I really got the results... 😄🎉. Once again thank you Mam for helping us
Solved all my issues. Thank you so much!!
Awesome, it was so nice and easy to understand. big appreciation and thanks to you for such easy video
Thank you so much! This is the best explanation out there. Really helped me.
Glad it helped!
Thank you so much ma'am for this. ❤️ how beautifully you explain each steps.
You made my day and i had the first successful docking output. Thanks for your great contribution!!! The least I can do is subscribe and subscribe and ...like!
Thank you so much for this video tutorial ....🤩🤗
your video is very nice and so easy to understand, please make video to docking metal coordinated complexes by using same tool
Thank you. Your efforts are appreciable
Hi, I am not able to save the file in pdbqt format.
I tried several times and continuously it is getting saved as pdb file. Any suggestions?
Thanks a lot mam...for your so detailed video❤❤
Explained in a very lucid way.
Thank you madam little faster u explained .
when i run the autogrid4.exe, and launch the dialogue box, the error in the cmd prompt : "Grid data file needs the extension ".fld" for AVS input" ; keeps coming up. can you help me out with this issue, i have been trying since a few days.
same here
Same too that's not working
Your video is 42 minutes but I took 42 hours to watch it again and again while working
Really a helpful video...clearly explained all the steps, thaks a lot.... is it possible for u to show docking with organic molecules?
Subscribed with much love and interest and enthusiasm
Thankyou very much. 🙏🏼🙏🏼
Very informative mam
Dear ur videos r v much helping
Plx make videos on simulation of docked complexes using Amber
Excellent organmed it can make possible by you only thank you so much
Hello.. Very nice.. ❤️Thank you😘👍
But how we can analyze docking results... I mean how we can dock the ligand to protein and see their interaction. Please explain 🙏
th-cam.com/video/-UBfDq1dcYQ/w-d-xo.html
Check it out!
@@organomed Once again Thank you so much ❤️🙏
Most welcome
How to find many ligand molecule are attached to a specific protein??
Is there any steps to determine..for ligand protein attachement??
Plss..help me mam...
You can visualize other ligands attached to protein using Discovery Studio.. For that you can check my AutoDock Vina Tutorial
Problem existed when I choose ligand at the grid..
Hello , at first I want to say thanks for this video. But I have question too. My question is, "what is the procedure to make distance between protein and ligand like chimera!! ".in my grid box, both protein and ligand are present, but I think, only protein must be present in grid box
As we all know that docking simply interaction between receptor and ligand molecule, before docking we do remove the water molecule and some other additional ligands molecule , and add polar hydrogen bond also, Afer that we dock between receptor and ligand molecules, and more negative sign give the good stability.....but sir my question is that in natural condition how water and additional ligands remove from receptor molecules and how will i add polar hydrogen also?
Thank you so much, a very good video and nice presentation.
Thank you
Thank you so much ❤️
This video was very helpful. Why does not ligand and protein files show up in the single folder. I save them on desktop but while choosing the file they do not show up as well.
In the last step, map files are not generating, and at the end, it shows autodock needs the extension of the docking parameter file to be ".dpf". Could please solve this problem?
thanks, excellent presentation
Thanks
Thank for your video! however, I found that your reference RMSD values were very high compared to those of RMSD values, respectively. Is there any problem??
Your videos are very good. I am getting error of bad window path name when I run autodock..what to do
Thankyou so much...loved this tutorial
maam my dlg file showed error and was of less kb size. thank you for the video it was really helpful.
Hello, your tutorial is very easy to follow, and it helps me a lot. I just wanna clarify, is the version of the autodock downloaded 4.0?
Yes.
@@organomed Thank you very much!
Excellent!!!!!
Bahut sai bahut sai 🥰🥰🥰💐💐🍫🍫
thank you!
Hello mam..... I am doing autodock but map files are not generating and showing as ERROR: Unknown receptor type: "Na"... Add parameters for it to the parameter library first!
I am not understanding where to change in the parameter library..... Pls help me. I really need your help.
Pls reply..
Excellent elaboration
Thank you!
Hello there. Your video is very helpful, but I'm stuck at the point of Run. When I launch the autogrid it doesn't not generate a GLG file in my folder and no maps either. In case its important, my vina items are also in the same folder where all docking-related stuff is. Kindly help. Thanks
I appreciate this tutoring - it was helpful and interesting!
One thing has been reeling in my mind since last month. May I know how to dock a metal-ligand, say, Palladium oxide or any foreign metal whose parameters have to be manually included in the AD4 parameters and bound.dat files, to a receptor (protein)? Can a molecular docking tutorial be featured, regarding this?
Thank u 😘😘😘😘 ,really appreciate ur efforts
So nice of you
Hello ma'am please tell us
The energy minimization or structure optimization of ligand (i.e. drug ) isn't necessary before doing docking?
when there is a need for structure minimization of ligand & why?
EM of ligand is usually performed before Docking and you can go with that.
Thank you for the interesting video, but might I ask, went come to the grid box it has specific value or just adjust until it fully covered the protein (for the blind docking)? Hope you can answer, thank you
Thank you for the awsome explanation
Hi...I have completed the first step of protein and ligand preparation ... But when i run the autogrid there is showing some error : that my autogrid.exe file need an extension ". fld" and map fike is also not generated . What does it mean...could u please help...
*file
Your docking folder is not present in C drive. Send the pic where you had saved your docking folder in mail.
@@organomed please provide mail Id so that i can send you pic...
organomed2020@gmail.com
thank you so much it helped a lot
Thank you for the very clear and elaborate explanation. Can you please present virtual screening
A tutorial on virtual screening using PyRx has been uploaded. Check here - th-cam.com/video/UIk6ISuS5Lk/w-d-xo.html
congratulaions you are very good
Thanks
thank you very much for this video
Awesome tutorial, thank you so much
Welcome
I don't know how to thank you maam, after a month I did it, Thanks a lot
Thank you for the tutorial. I am not able to generate the protein.SA map which is why my docking run is not getting completed. Please tell me how to solve it.
P.S. gpf file has the SA as receptor type and successfully completed forming .glg file.
Thanku mam.... Its very helpful for us
Most welcome 😊
Thank you for this video
This video is very helpful. Thankyou.
But I am not able to launch Autogrid at the end. What should I do?
Mail me the pic of your docking folder location.
@@organomed Yes, Sure
Please, explain how do docking with protein,which has Zn ion in active side(Adenosinedeaminase).
Plz make a video on analysis of docking
mam in this video ligand is not bind still I just want to understand the later steps too for ligand binding
Hi,
I am trying to dock a compound which contains Copper. I got this error
while performing autogrid.
Can you please help me with this error :
\autogrid4.exe: ERROR: unknown ligand atom type Cu
add parameters for it to the parameter library first!
This is because some parameters are missed in Autodock version 4 . I will suggest you to go through this link and read properly -autodock.scripps.edu/faqs-help/faq/how-do-i-add-new-atom-types-to-autodock-4. Hope you had followed other steps properly .
@@organomed thank you a lot
Thank you so much.it really helpful to me
Really interesting, thank you very much
Best wishes dear
Thank you so much for your useful lecture. When I run blind Auto-docking, I have face one problem, the gdl file is not complete, it only 7 pages. also when I prepare the molecule and need to save it (write options) Not involved ANISOU, which started from ATOM. I wait your reply, Many thanks
Dear Madam I have done blind docking following this video and I am very happy to inform that it ran till the end. My suggestion is that if you could explain the dlg file in more detail and any reference or literature on it. At some points I had to rewind a number of times because it appeared a little bit fast for a new user like me. also I want to know which information of the output file is required for publication . kindly give me your email address if possible . Previously I have done modeling with DS suite by Accelrys and never used free softwares like autodock,gromacs ,pyrx etc. So I am very much interested in your videos which are very helpful. Thanks
after installing mgltools we are getting Vision 1.5.6 ans CADD1.5.6. What is the use of those icons ?
organomed2020@gmail.com
@@indranisarkar3901 they are for visualization
Thank you for your informative tutorial,
I try to make a docking for interaction between chromatographic stationary phase and the analytes however the map and glg file did not appear
Do you have any solution for this problem, please Thsnk you in advance
Thank you very much ma'am.
How we will identify one lead molecular out of 100 or 1000 or more molecules
Grt .....I m thankful to u
Hello, thank you for your autodock tutorial. I am curious that why we have to delete chain B at the first time in preparing protein? Also, when i try to save the ligand as the dpf. file, it doesn't save as dpf file. Thank you.
Thank you
I am trying protein 2QMJ with acarbose but Docking results are not generating
But for others protein the results are generated.
How to dock 2QMJ with acarbose please help.
I was using ozempic as my ligand against the GLP-1 receptor and i didn't have not got any results.
First my ligand(ozempic) didn't show it's root.
I don't know what to do
We use molegro molecular viewer to remove water molecules...
Thank you so much, it's verry important
Ma'am, could you please explain how to use haddock
I want to do antibody interaction and that would be useful
So please ma'am
Your videos males this look so easy
nice its really helpful for me
Mam only ten confirmation hi possible hai usse jyada confirmation ki energy nahi mil sakti.
When i do select grid ~ macromolecule ~choose~select protien then show a different interface like as error please help