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AutoDock Tutorial || Molecular Docking || Best and Easy Way ||
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- Опубликовано: 2 авг 2020
- 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.scripps.edu/downloads
AutuDock - autodock.scripps.edu/downloads
Open Babel - sourceforge.net/projects/open...
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.
You can follow OrganoMed on various platforms -
INSTAGRAM : / organomed2020
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TWITTER : / organomed
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#moleculardocking
#autodock
#docking
#blinddocking
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
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.
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!
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!
You explained each and every step so well, it cleared most of my doubts regarding autodock
Thank you for that.😇
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 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 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.
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!
I'm happy to come across this tutorial it's a blessing.
Thank you so much for making this video
I am watching it after 3 years and it is very helpful for me
This is the best video have ever seen about docking
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! This is the best explanation out there. Really helped me.
Glad it helped!
Awesome, it was so nice and easy to understand. big appreciation and thanks to you for such easy video
Thank you so much ma'am for this. ❤️ how beautifully you explain each steps.
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!
You are just growing amazing day by day❤❤.. best wishes...
Thank you so much 😀
The only tutorial that proved helpful! TYSM
Glad it helped you!
Thank you. Your efforts are appreciable
Thank you so much for this video tutorial ....🤩🤗
Solved all my issues. Thank you so much!!
This is the new aspirant of docking learner sooo I hope that I’ll learn more from you inshallah
thank you so much, very helpful much appreciated.
Its really well detailed and clarified regarding steps to steps of auto docking right from the downloading the softwares to finally building a molecule.
😮❤❤❤❤
This beautiful and smart lady has helped me so much. God bless you
Glad it helped you!
Subscribed with much love and interest and enthusiasm
Fantastic video... no words tq..
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
Thankyou very much. 🙏🏼🙏🏼
Excellent organmed it can make possible by you only thank you so much
Thanks a lot mam...for your so detailed video❤❤
Thankyou so much...loved this tutorial
Really a helpful video...clearly explained all the steps, thaks a lot.... is it possible for u to show docking with organic molecules?
Explained in a very lucid way.
Thank you I really got the results... 😄🎉. Once again thank you Mam for helping us
thank you so much it helped a lot
thank you very much for this video
Thank you so much, a very good video and nice presentation.
Thank you
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?
Thank you for this video
Thank you very much for the tutorial, it was truly helpful! But I keep getting an error: insufficient grid points. Could you please tell me how to avoid that? Thank you.
So if I was to work with another protein other than 6vww, do I create a whole new folder for it or I use the same docking folder?
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??
Thank you for the awsome explanation
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
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 you so much ❤️
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
hi again
the structure of ligand , must be optimized by another program such as hyperchem , gaussian...(this is step before docking)..or the optimisation is not obligatoire
Really interesting, thank you very much
your video is very nice and so easy to understand, please make video to docking metal coordinated complexes by using same tool
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.
Awesome tutorial, thank you so much
Welcome
Hello, Thanks a lot for your video. I have a couple of questions regarding docking with my protein. Please can you guide how to do docking with a heme protein like P450. I have tried, and it only works if I delete the heme and other attached groups from the protein molecule. Secondly, I have a charged ligand with a NO2 group attached to a cyclic hexane ring. The N has a +ve charge and one of the oxygen attached to the nitrogen with a single bond has a -ve charge, while the other N is double bonded to Nitrogen without any charge. How to prepare this ligand in its charged state. The software prepares pdbqt file, but docking always gives errors.
Can we perform docking on both chains or only A chain is required?
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.
Please, explain how do docking with protein,which has Zn ion in active side(Adenosinedeaminase).
Thank you so much, it's verry important
Thanks 4 the tutorial. But how to convert your docking result to pdb format ??
Thank u 😘😘😘😘 ,really appreciate ur efforts
So nice of you
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
Thank you so much.it really helpful to me
I have a problem on my autodock tools, I have installed it following the steps, the software is working but am not able to view the molecule in the display area this is the message on the coding viewer "swig/python detected a memory leak of type 'BHtree *', no destructor found".
can anyone help me out?
Hi, I had no problem in installing and converting the target protein to pdb-pdbqt format, but the display of the drug in the pdb format was not same as what you showed. Pls reply as soon as possible.
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
Hello
I installed all the software for docking you mentioned in the video but my autodock is not working properly. It is showing loading molecules only 8% complete than disaper. What can I do?
Your videos are very good. I am getting error of bad window path name when I run autodock..what to do
How could I do docking for new compound that are not in pubchem
Hi,
In my receptor it has metal ion Er. Since it is not defined it the autodock parameter file I add it. And I was able to generate my glg and dlg files. But when trying to analyze(when try to get vina out usin cmd) an error appear "protein.pdbqt: ATOM syntax incorrect: "Er" is not a valid Autodock type, Note that autodock atom types are case sensitive"
Could you please give a solution to this problem.
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?
Thank you very much ma'am.
How we will identify one lead molecular out of 100 or 1000 or more molecules
thank you so much mam. Actually , i am encountering a problem with syntax error. my compound is having Si atom in it. Error is atom syntax error. How can i resolve it?
Thanku mam.... Its very helpful for us
Most welcome 😊
how can I create a different folder for each docking I am going to run for example, can I use the same folder for different samples?
nice its really helpful for me
How to add charge to zinc ion at the active site of the receptor before docking? Tried adding manually to the pdbqt file but during docking, it is showing error.
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?
Very helpful
Madam my protein have 5 chains is there, so I will delete 4 chains or I use 5 chains for docking?
Excellent!!!!!
My autodock process manager shows up for only one second and i never get results but there is no error showing up? What should I do?
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.
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
Thank you so much.
Thank you
Please tell me is it necessary k hm pdb say structure lain..main jb pdb wali ID use krti h to mera result ni hta..
Lakin jo main ny homology modeling su structure nikala tha wo use krskti h???
Please tell me
Very informative mam
thank you so much mam😍
Thank you so much❤
during running the autogrid it is asking that need extension of of FLD file - what it is? how to solve this problem
Best wishes dear
how to separate the conformers as single complex file, by following the analyze process ?!
Dear ur videos r v much helping
Plx make videos on simulation of docked complexes using Amber
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!
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.
thanks, excellent presentation
Thanks
From where i get autogrid, can you suggest me
Hi if anyone can help me when I run Autodock vina " the results of the command prompt give me error; parse error on inline 7150 in file "protein.pdbqt" :ATOM syntax incorrect "Mo" is not a valid AutoDock type. Note that autoDock atom types are case-sensitive. How I can fix this error