Molecular Docking Tutorial: AUTODOCK VINA - PART 1 | Beginners to Advanced 

thank u Sanket B.. excellent and more useful both of docking videos

I think I'll put your name in acknowledgment, you are the only one who helped me in learning which I was roaming around behind everyone... Thanks

I never thought i'll enjoy learning simulations so much. Thank you for making it so simple and easy. :)

These two videos have been really helpful for my work. Thank you so much.

hello, i find molecular dynamics hard to learn as i had no prior experience with coding and linux (what my teacher recommended me to use), videos like this makes it very easy for me to understand the concept and how to do it. THANK YOU FOR THE VIDEO!

i want to give you the credit if I got a paper published like literally ...Extremely helpful

I love this. It is so helpful and explanatory.

the best video i have ever watched so far thanks a lot for your kind efforts

Very useful both parts for autodock vina learning

thank you sir , you explained each and every step very clear .

You are doing a very good job. Keep it up Dr.

superb video..your way of explaination is so clear

Why do you skip some steps like energy minimization of ligand and protein and charges added to ligand

This video series help me a lot

Hello Sir! How to prepare script for multiple ligand docking?

Very nice video sir.... Ur explanation was very clear ... Thanks a lot sir

great video content about docking

Honestly I appreciate so much your video thank you

Great tutirial and very informative one. Kindly if possible add ligand and DNA docking tutotrial. Sir it would be great job on your part. Thanks regards

Very well explained .. sir thankyou so much for ur efforts..

At 17:55, Spacing parameter is set 0.375 A, but this is not used by AutoDock VINA. Changing this parameter affects the grid box size. So even you attempt to perform site specific docking, the docking is going to be blind docking due to this parameter. I am not able to get the clarification about this parameter while docking except VINA official tutorial has this option set as 1.

you are doing grat job. Could you prepare a molecular docking video for ligand-based drug design.

Can you make a video about how to minimize energy please

like your tutorial video sir, very helpful. Thank you so much 😇🙏

Thanks for the amazing explanation

Sir, very nice video Can you please make a video in which you explain how adding a metal ion ( in my case is tin)

I'm in bsc 2nd year and I could understand anything sir ... I'm just curious why did you remove the water molecules and add polar hydrogen to the protein ??

Sir, at 9:25 you add Kollman charges to the protein. However, at 15:23, when you load the protein macromolecule, you click on 'no' for preserving Kollman charges. The next popup box states that Gasteiger charges were added. So, should we add Gasteiger charges for the protein?

It´s so nice your video, Sr! Thank you

I have a doubt. I guess The grid box has to be formed around the active site residues by changing the x, y and z axis values so that the interaction can be calculated correctly,

Thanks for great tutorails! Small question - why do not you add all hydrogens but only polar ones?

Thank you Sanket Bapat. Both the videos are very neatly and clearly presented. Highly informative. But once after docking how are we to interpret it in the paper. Any suggestions or advice regarding the same.

What about chimera or autodock and pymol is more effective...thank so much Dr.sankat🎉🎉😊

Thanks for this video!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! I love you

Thank you sir for such a nice video. One question- if we don't know the active site, why we are not enclosing the whole protein inside the grid by changing dimensions.?

Before preparation both protein and ligand minimize step is important

Sir, Amber 18 pe kaise simulation hota hai....iska video banaiye kabhi 🙏

Amazing it's educating thanks

It's very helpful can make a tutorial or multiple ligand docking and results interpretation on auto dock instead of pymol

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?

Can anyone help me out with the installation , I seem to have problem with finding the vina folder in the path hence not able to attempt docking

I was done project work the same topic Sir.

Very well explained sir

Great job dear Prof. highly appreciated. I am quite new to molecular docking and trying to perform docking of activated carbon and a drug using your video as a guide. Will it be possible?

you are just pathfinder for bioinformatics learner.

Very informative Sanket B.

Thank you for your helpful videos Dr. Sanket. I have a question. Is Autodock vina flexible or rigid docking?

Very nice information Dr. Gajanan Dongare Akola Maharashtra

Hi very informative tutorial on AutoDock Vina but I have a question which is that what about if we don't know about the ligand binding site of our protein so how can we set the grid?

Thank you doctor🎉

Good day to you sir. Thank you for this excellent interactive session. I have a query, What is to be done if ligand profiles are not seen in the downloaded material from PDB.

I have done docking in vina by coding only..autodock is GUI, isn't Vina acessesd by coding only?

Im performing docking on a known active site so i limited the gridbox around the active site only. Some of the conformations i got after docking were outside the grid box. Is that normal?

Hi thanks for this, came at the right time! When adding the grid box, is it generated automatically at the binding pocket or will have to adjust it? if so, how do i ensure its the 'correct' coordinates?

It says could not open "config.txt" for reading while clicking enter from (8:35). Please help

Could you make a video showing how to dock in Vina Auto-docking using some flexible active site waste? I need my molecule to interact with specific residues and I don't know how to do it. Please.

Is there any rule regarding which chain should be kept and which one should be deleted ?

sir I wanted to know..if the same thing can be executed in ubuntu system

Can DNA-Protein docking be performed in Autodock? Please suggest a suitable tool for building DNA 3D structure

my protein file is not saveing as the pdbqt so what should i do

Can you please let me know why do we add polar hydrogens and kollman charges?

Hi Dr. Sanket. I am an IBDP 2 student. For my school project I need to conduct multiple ligand simultaneous docking. I was able to conduct single ligand docking but am unable to understand how to do MLSD. Can you please help with instructions on how to do this. Thank you

Sir plz make a video of docking by arguslab ...i really need it now

Thank you very much, well explained. Is the Auto dock vina App free?

Sir, can we used ligand file prepared in autodock tool in Vina and what about energy minimization step?

It is necessary in autodock to kept the torsion agnles of ligand less than 6?

if I follow the step by step of your docking lecture, then can i make the HLA/HLA-DBR and epitope docking properly for vaccine design??

I am not getting the grid option in my Python molecule viewer. Can anyone tell me, how to get it?

If I use a receptor that I have already known the binding site with a reference ligand, how can I set the grid box in that binding site only for docking with other molecules?

My pdb file is getting downloaded in the form to words how can I get in form of image

Should we follow the default grid box dimensions mentioned in the autodock vina ? Wouldn't it be correct if we first checked literature for the docking site and then changed the dimensions of the grid box? Dr. Sanket , could you clarify this ?

Hi! Tab with Ligand icon not available to do ligand preperation in MGL tool. Appreciate your help regarding this how to go about

Hi! Thank you very much. i learned a lot from your tutorial. May I ask, how can I specify the number of docking runs in Autodock Vina? Is it possible? Coz I am planning to dock at 70 runs.

Hi! very helpful video indeed. I have one query which is my SDF file is not getting recognized as a SQLCE database. how do i overcome this error? Kindly help..

Can I get the part 2 link please

Sir please can u name any inhibitor for hgd gene for alkeptonuria disease

Devudu swami nuvvu.. 🙏❤

Thank you Sir

Can we perform docking with metal complexes ( Pt complex)?

Hello sir, when i click on grid and selecting the protein then get error, showing protein pdbqt has one or more hydrogens with no bonds. Plz solve this problem

Can you please guide with homology modelling using Modeller???

sir can you please tell me how to determine mutation rate of covid19 using bioinformatics tool? and which tool can be used?

Auto dock vina or auto dock 4 different h.. Lakin unka page same kiun h..koi bta skta h..

Sir can u plz give tutorial on discovery studio ?

Hi Sanket, do you know how to calculate the binding constant or inhibition constant?

Sir,can you tell how to determine ki for inhibitors using autodock

in ligand prep you made an error ! ypu must do a torsion before save it as pdbqt

In docking...grid macromolecule protein are choose..then show error....so, what do i do now.... Plss..help me..

Hey very nice and clear presentation. Wanted to ask one question so the final poses that you visualise in pymol and if we suppose find the first pose as the best docking pose how do we save it and use for showing it in power point?

Thank you so much for your video Dr. Sanket. Firstly I hope you are healthy and safe. I'm trying to perform a molecular docking but I have an error while trying to save the PDBQT file: Unable to assign HAD type to atom Mg Unable to assign valence to atom protein:B: MG2003:MG type = Mg Unable to assign HAD type to atom Mg Unable to assign valence to atom protein:D: MG2003:MG type = Mg By any chance, do you know how to solve it? Thank you so much in advance!

i use pyrx for docking, and use multiple ligands i download them from zinc database (nubben database for natural compounds), i do minimization and docking but when finish the result are encodede for the compound it just codded the energy , and they are 2332 compound how can i know the compound crosspend to each result???

Thanks for such a nicely presented video, especially for beginners. However, during the protein and ligand preparations, i am unable to save file in pdbqt format. kindly guide through some tips, which could work for me

Cant I do docking in the autodock tool instead of prompt command?

can anyone please explain my following question? this particular protein "4mzi" in this video has some missing residues in its side chain. so is it possible to do docking without fixing it ? in this mgl tool he didnt fix the missing residue. will that make good docking ?

thanks for the video!!! how can i choose only the active site of the protein to do the docking? and how to find out where the active site is?

Sir.. Everything is useful in this video. But am unable to download PyMOL. My system can't allow that to instal. So, kindly send the ligand format file, sir.

PLZ MAKE A VIDEO ON CABS DOCKER

Respected sir need help The command shows the program is not recognized as an internal or external command operable program or batch file what is the solution for this problem

hii.. I need your help. everytime I am trying to save as pdbqt format, my file is being saved as pdf.. could you please tell how to resolve this problem

Hello Sir! thank you for your videos,i have a question ,when i drug the pdb files into Autodocktools software,it occurs a error “4mzi.pdb does not exists”,hope you can help me to solve this problem,thank you!