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

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

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

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

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.

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

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

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.

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🥰

This is the best video have ever seen about docking

The only tutorial that proved helpful! TYSM

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

Very informative clear explaination and make more videos on molecular docking waiting for your videos

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

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

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

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

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.

Thank you so much ma'am 🙏❤️

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

Solved all my issues. Thank you so much!!

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.

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

Fantastic video... no words tq..

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.

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

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

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

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 🙏

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?

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?

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!

Hello madam We need to cover only the protein with the grid box or both the protein and the ligand.

Is the co crystal ligand is not removed is this can make issue or not?

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

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

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

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

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. Your efforts are appreciable

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

This video is very helpful. Thankyou. But I am not able to launch Autogrid at the end. What should I do?

Subscribed with much love and interest and enthusiasm

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

Thanks 4 the tutorial. But how to convert your docking result to pdb format ??

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?

Explained in a very lucid way.

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.

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

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

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?

Madam my protein have 5 chains is there, so I will delete 4 chains or I use 5 chains for docking?

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

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?

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

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?

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?

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.

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

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

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..

Thank you

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

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

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...

Thank you madam little faster u explained .

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

Can we perform docking on both chains or only A chain is required?

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

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?

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.

Thank you for the awsome explanation

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

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

hi, thanks for such an informative video. Best wishes. i m facing a problem, that .mep .glg and .dlg is formed after running the grid and docking files. pls help regarding this issue. Thanks again

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?

Thankyou so much...loved this tutorial

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

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?

i am trying to save the files in .pdb format but by default it has been saved in biovia. how do I resolve it?

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.

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

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.

madam, don't we have to do energy minimizing before we run autodock

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?

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.

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.

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

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?

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

Really interesting, thank you very much

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.

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?

Thankyou very much. 🙏🏼🙏🏼

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

Thank you so much.it really helpful to me