AutoDock Tutorial || Molecular Docking || Best and Easy Way ||

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.
You can follow OrganoMed on various platforms -
INSTAGRAM : / organomed2020
FACEBOOK : / organomed-102331571565167
TWITTER : / organomed
TUMBLR : / organomed
#moleculardocking
#autodock
#docking
#blinddocking

[@ferb.3045]

OMG thank you so much this has solve the problems I´ve been having for a month!!!! you are amazing

[@organomed]

I am really happy to listen that this video is solving your problems.

[@ferb.3045]

@@organomed you are also a great teacher so that helps too

[@organomed]

@@ferb.3045 Thanks

[@aqsamuzammil7791]

Finally, I understand Autodock after this tutorial..... Before that, I have tried at least 5 different tutorials on youtube. YOU ARE AWESOME

[@organomed]

Thank you

[@shivamdixit5304]

Can u help me please

[@nwnikhil9712]

Thank you so much for making this video I am watching it after 3 years and it is very helpful for me

[@apoorvalongtin]

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

[@organomed]

Glad to hear it!

[@yaseenjanalchemist8026]

This is the new aspirant of docking learner sooo I hope that I’ll learn more from you inshallah

[@swaritagopal8722]

Thanks a ton. I was really struggling with the last step. Excellent way to clear for someone new in this field.

[@organomed]

Pleasure to hear it!

[@peter_dockit]

This is the best video have ever seen about docking

[@sharpgrin4345]

This beautiful and smart lady has helped me so much. God bless you

[@organomed]

Glad it helped you!

[@azizarahman8525]

The only tutorial that proved helpful! TYSM

[@organomed]

Glad it helped you!

[@barshapaul8344]

You are just growing amazing day by day❤❤.. best wishes...

[@organomed]

Thank you so much 😀

[@chem412]

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.

[@radhikasharma4228]

Thank you so much for this video tutorial ....🤩🤗

[@hana_koo99]

Thank you for making this tutorial, I've completed all the steps and get the results! Thank you so much 💛

[@safaeerraouan2861]

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

[@user-zb4sj2lv3n]

Its really well detailed and clarified regarding steps to steps of auto docking right from the downloading the softwares to finally building a molecule. 😮❤❤❤❤

[@hamzaallal1867]

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.

[@organomed]

Glad it is helpful! Happy to hear it.

[@hanstsahnang4533]

I'm happy to come across this tutorial it's a blessing.

[@ruchisingh2177]

Thanku so much for this video ..I was having lot of problems earlier ..but the way u mentioned every details so nicely .. thanks

[@organomed]

My pleasure!

[@madhujeevan7671]

Fantastic video... no words tq..

[@lifeinsequence]

Solved all my issues. Thank you so much!!

[@dhwanipatel7626]

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 😇

[@rudraacharya4061]

You explained each and every step so well, it cleared most of my doubts regarding autodock Thank you for that.😇

[@noursh6783]

thank you so much, very helpful much appreciated.

[@dhwanipatel7626]

Thank you I really got the results... 😄🎉. Once again thank you Mam for helping us

[@jaidevgollakota1833]

Thank you so much! This is the best explanation out there. Really helped me.

[@organomed]

Glad it helped!

[@rashmisharma_2639]

Thanks a lot mam...for your so detailed video❤❤

[@nandkishorbawage5343]

Thank you. Your efforts are appreciable

[@resinwithlove]

Thank you so much ma'am for this. ❤️ how beautifully you explain each steps.

[@kapildangi9312]

Thankyou very much. 🙏🏼🙏🏼

[@great2395]

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!

[@dr.mzsiddiqi8002]

Awesome, it was so nice and easy to understand. big appreciation and thanks to you for such easy video

[@aritrabiswas2268]

Explained in a very lucid way.

[@yaseenjanalchemist8026]

Your video is 42 minutes but I took 42 hours to watch it again and again while working

[@yaseenjanalchemist8026]

Subscribed with much love and interest and enthusiasm

[@powervoice5348]

Thank you madam little faster u explained .

[@ayeshafawad-px3qo]

Dear ur videos r v much helping Plx make videos on simulation of docked complexes using Amber

[@sharanbiradar8925]

Very informative mam

[@dhanudhanunjay7652]

your video is very nice and so easy to understand, please make video to docking metal coordinated complexes by using same tool

[@sharanyapaul9819]

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?

[@gaazijavaid]

Problem existed when I choose ligand at the grid..

[@deepah.k1537]

Excellent!!!!!

[@aravindnesaragi3980]

Really a helpful video...clearly explained all the steps, thaks a lot.... is it possible for u to show docking with organic molecules?

[@rickyseldon9031]

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.

[@victoriamelts9956]

same here

[@safaeerraouan2861]

Same too that's not working

[@ankitachetia5129]

Thank you so much ❤️

[@khanubaidurrahman8094]

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.

[@krabbykat9918]

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

[@anahitbakaryan6541]

Please, explain how do docking with protein,which has Zn ion in active side(Adenosinedeaminase).

[@prachijain-c2i]

Your videos are very good. I am getting error of bad window path name when I run autodock..what to do

[@ushasingh9944]

Excellent organmed it can make possible by you only thank you so much

[@ApurvKhombare]

Ligand is not bound/interact with protein? What is that?

[@pallavisangle4787]

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...

[@organomed]

You can visualize other ligands attached to protein using Discovery Studio.. For that you can check my AutoDock Vina Tutorial

[@shivamdixit5304]

When i do select grid ~ macromolecule ~choose~select protien then show a different interface like as error please help

[@muttum9357]

during running the autogrid it is asking that need extension of of FLD file - what it is? how to solve this problem

[@gavinahaisibwe7952]

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

[@meenublossom6860]

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 🙏

[@organomed]

kzbin.info/www/bejne/Y4all3enZsmWj7M Check it out!

[@meenublossom6860]

@@organomed Once again Thank you so much ❤️🙏

[@organomed]

Most welcome

[@emelynstanica4612]

hello! I cannot see my protein in black screen. Can you tell me why?

[@naveenmurugan4055]

We use molegro molecular viewer to remove water molecules...

[@vivekanandinspire4883]

mam in this video ligand is not bind still I just want to understand the later steps too for ligand binding

[@iramhussain1710]

Excellent elaboration

[@organomed]

Thank you!

[@NourElyakineamraoui-wf5wy]

thank you very much for this video

[@abumalik67]

thanks, excellent presentation

[@organomed]

Thanks

[@user-qk2hg3we7v]

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?

[@samarendraningthoujam8909]

Hi, I am not able to generate GPF File in auto-grid output step. Instead, it gives only one file without any format. What is the solution?

[@athirat4021]

Thank you so much, a very good video and nice presentation.

[@organomed]

Thank you

[@SolomonMakanjuola]

Thank you for this video

[@ReadwithFacts]

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..

[@yaseenjanalchemist8026]

How could I do docking for new compound that are not in pubchem

[@yvonnesoki4825]

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?

[@meghanapg4157]

How to proceed if the protein doesn't fit in the grid box?

[@karunsodah9181]

Plz make a video on analysis of docking

[@mufaspismail9885]

Thank you

[@purvakhodke4386]

Thankyou so much...loved this tutorial

[@sourabhjain3356]

U have explained everything very wonderful but I m not getting how to generate Config file..

[@umumiyetlefutbol7322]

How we can understand that which ligands we should study with

[@nehabhandari7747]

maam my dlg file showed error and was of less kb size. thank you for the video it was really helpful.

[@Sarahbahh]

thank you so much it helped a lot

[@GurpreetSingh-ic5uz]

Grt .....I m thankful to u

[@NourElyakineamraoui-wf5wy]

Thank you very much for this video, .... I carried out all steps but when I arrived at grid steps exactly "set map types " failed please, can you answer me what was the problem?

[@safaeerraouan2861]

i have the same problem now, can u respond pls

[@indranisarkar4313]

Thank you for the very clear and elaborate explanation. Can you please present virtual screening

[@organomed]

A tutorial on virtual screening using PyRx has been uploaded. Check here - kzbin.info/www/bejne/i3rOZ3yJqrhogs0

[@user-rg5og3bc3i]

There is a problem that after run autogrid, maps and glg files are not generated. What step i have missed. Can you please help me to resolve this issue

[@meenublossom6860]

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...

[@meenublossom6860]

*file

[@organomed]

Your docking folder is not present in C drive. Send the pic where you had saved your docking folder in mail.

[@meenublossom6860]

@@organomed please provide mail Id so that i can send you pic...

[@organomed]

[e-mail]

[@abdeldjebarhasnia1788]

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!

[@organomed]

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 .

[@abdeldjebarhasnia1788]

@@organomed thank you a lot

[@gaazijavaid]

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.

[@sanketkore9846]

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?

[@organomed]

EM of ligand is usually performed before Docking and you can go with that.

[@user-tr7jv9up3m]

you have deleted one chain from your protein. i have many chains in my protein how i will know which protein should be removed?

[@balarampaul3897]

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

[@rumeshnelumdeniya557]

Thank you for the awsome explanation

[@fintouf]

I don't know how to thank you maam, after a month I did it, Thanks a lot

[@juhidutta6121]

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.

[@horanghae4649]

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?

[@organomed]

Yes.

[@horanghae4649]

@@organomed Thank you very much!

[@pujabharti4781]

Thanku mam.... Its very helpful for us

[@organomed]

Most welcome 😊

[@princyv2198]

While write the protein in PDBQT . the error showing like cannot create the pdbqt. All atoms do not have an autodock element field ... Why

[@ogunoluwamayowa4749]

Awesome tutorial, thank you so much

[@organomed]

Welcome

[@yvonnesoki4825]

I do not ger map files but i also do not get an error. What should I do?

[@knowledgeseeker9757]

Hello ma'am why my docking score changes everytime I run?

[@kavithasusan9842]

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.

[@farahnatela732]

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

[@sonetdthomas4175]

The dlg file showing "I can't find or open 1". how can i fix this problem

[@daphishasohtun9367]

Ma'am I got error while register that auto dock can u please kindly help what to do

[@chloeburbank4045]

hello. i am having a problem with running autogrid. i followed all the steps in the video, and even tried removing hetatm but i keep getting this error when running autogrid: D:/Docking/autogrid4.exe: ERROR: Unknown receptor type: "Na" -- Add parameters for it to the parameter library first! can you please help me? thank you

[@Pablo-tt5kv]

my MAP files did not generate :( im not to sure what im doing wrong i followed everything exactly