Molecular docking for Beginners | Autodock Full Tutorial | Bioinformatics

The molecular docking approach can be used to investigate interaction between a small molecule and a protein at the atomic level, which allow us to understand the behavior of small molecules in the binding site of target proteins, and biochemical mechanism in b’n protein and ligand molecule.
This video will provide you full step by step manual on Protein-ligand docking using Autodock
MGL Tools: mgltools.scripps.edu/downloads
Autogrid4 and Autdock4 : autodock.scripps.edu/downloads...
Open Babel GUI: github.com/openbabel/openbabe...
Literature:
www.ncbi.nlm.nih.gov/pmc/arti...
autodock.scripps.edu/faqs-help...
www.sciencedirect.com/topics/...

[@ChemWonders]

This video will stand as a landmark in my future studies on docking. Well done and Thank you.

[@abdulmalikaliyu8876]

I went through your presentation sir and I was able to understand it. Thank you very much. We plead for more like this.

[@jaannawaz2007]

Ur welcome

[@abhijeetaher4701]

Dear sir, nice presentation i want to do ligand ligand docking to find out hydrogen bonding possibilities in two different ligand to study interaction, how i can do this

[@mollylu3638]

THIS IS SO HELPFUL! So clear! I have seen other ones which the youtuber makes mistakes and go back and forth, but with this one I really had the peace of mind and it worked in one try! Thanks so much for taking the time to make this! Already subscribed and will be going through other tutorials!

[@alannah3245]

Amazingly clear tutorial! Finally got autodock working!! Thank you so much!

[@kbaitsi]

Really good tutorial, not just what to do but also why. Thanks!

[@ajaymanaithiya5014]

I have saw various auto dock videos but your videos are so good and also discuss what would we facing issues during docking and you solved these issues during videos. thank you for giving CMD for docking. because i have facing python she'll error. Thank you very much Sir for making these videos. Most of people made the video but doesn't tell about issue but only your videos I saw which have discussed about also issues along with solve the problem. THANKS ❤️

[@JaspreetKaur-ry2nb]

hi i am facing python shell error please help me in rectifying it

[@lorenchang2638]

Hello, Autodock reported some residues are missing atom. Actually I could see a non-bounded atom near residue. Guess need to add a chemical bond in between. What should to do next?

[@DrFoz-dv7hg]

what is the best docking tool for peptide interactions with protein or protein-protein interactions

[@mariamhussain5142]

Very useful and easy to follow, Thank you

[@ankitajalan4568]

Hello sir, thank you for explaining so nicely. Kindly explain how to determine probable site of binding. I m working with bovine serum albumin and am finding it difficult to identify site I and site II. Please help me. Thank you.

[@rajalakshmimanivannan3503]

Thank you so much for tutorial. It was very useful for beginner and even non biology majors also understood clearly.

[@jaannawaz2007]

Glad it was helpful!

[@raniaadhamira2954]

Hi thank you for good video ! I want to ask, what if we put xyz randomly as long as the ligan in the cube ?

[@petelok9969]

Hi great tutorial. I have a question. I typically use a config file but it doesn't contain any information about the GA parameters, so I take it I'm using default patameters? Can I put this information into the config file or can I put it in as a flag into the command lìne? Regards Peter

[@dashrathkondhare1136]

Many thanks for wonderful presentation.

[@tushardhyani3931]

Thank you sir for this, this is really helpful. please keep posting more content like this.

[@jaannawaz2007]

Thank you, I will...

[@bestofluck2225]

Wow!! Thanks a lot sir, I asked for this last time. It's a great to learn from the begining. Now I would like if you make MD simulation that will help me in my studies. Thanks in advance.

[@jaannawaz2007]

Thanks For Watching... Soon we will

[@ni-hamdeen5994]

How did you get the amino acid in the PyMol ? Can you show this?

[@wafaeaubrey838]

Hi, thank you sir for your clear tutorial. I actually want to learn how to docking so I tried to reproduce your example but i found a problem when i input the ligand.pdbqt file in Autodock tools. It send me this message: error parsing the following line in pdb: Atom 1 C LIG 1 22,000 40,000 32,000 0.00 0.00 +0,055 A Even if I followed what you did step by step. I don't know where is the problem, I even tried with others molecules ligand but the same thing occured. Can you please reply to me. Thank you

[@RAVISINGH-hd8hf]

sir how can we keep a fixed conformation that is S or R of ligand while in ligand preparation step

[@user-gg7gw7yf4w]

It is very very good! Thank you for work!!!

[@DrFoz-dv7hg]

I wonder if the best conformation is the one with the highest affinity or the one with more hydrogen bonding as explained by others like Dr. RAVIKUMAR CHANDRASEKARAN and it could have a lower affinity. would you explain, please

[@efedogukandincel2959]

How can you validate your docking method in Autodock / Autodock Vina. Normally, we perform docking process with co-cristalized ligand of crystal structure and calculate RMSD value. If it is less than 2A we can accept that our docking method is good. In autodock we get different rmsd values, reference rmsd and cluster rmsd etc. In publications how'll we state the validation of our model?

[@shamalidilhara8505]

Thank you so much sir. Its a very helpful video😊

[@aravindnesaragi3980]

Hello sir, Thank u for ur useful information... but i m getting error while repairing proteins, can u plz suggest me what shall i do?

[@kiranvaghela636]

Hello sir, Will it be okay, if i add polar hydrogen and then i perform repair of atoms in protein structure of receptor to prepare receptor for pdbqt format?

[@diagnoville6856]

Thank you for the video. How do you dock two proteins? Not protein and ligand

[@BIOLINEHK]

Thanks for video, could you please tell me, in my case why it shows error "receptor.maps.fald"?

[@cowboycatranch]

There is an AlphaFold 3D structure of my protein of interest in UniProt, but I can't find it in RCSB Protein Data Bank. What can I do?

[@neerajm3049]

Thank you very much. So helpful video

[@vippanchal8]

Good job! I really liked the tutorial. grateful.

[@jaannawaz2007]

Glad you enjoyed it!

[@GracielleFreitas]

Hi, when i try to remove the heteroatoms my program open a windows with python error. Do you know this error and do you know how to fix it? I have to do this docking because its my homework from college. my ligand stand so far from the protein and i dont know what to do about it :(

[@eshwarb2489]

Hi, I have a issue. I'm not able to get docking results as it show error like, FATAL ERROR: ERROR: 3778 records read in, but only dimensioned for 2048. Change "MAX_RECORDS" in "constants.h". Can u please suggest how to rectify this error ?

[@emilijaskrodenyte8341]

Hello, my input into Open Babel GUI was SDF file of N4-benzoyldeoxycytidine and when I want to convert it into pdbqt file, it says that 0 molecules were converted. Can you help to understand what is wrong? Thank you sir

[@thaoha8446]

Dear sir, the fourth amino acid which you selected was Lysine (270) and in the excel sheet it was given for Serine. Please help me with this. Thank you a lot sir.

[@ashirashid5950]

Hi i made lipid bilayer using charmmvsoftware and now opened its pdb in autodock. I am tryingbto add hydrogen atoms but getting error message from puthon saying the presence of several non bonded atoms. Please guide me how to fix it.?

[@ameracosmetics]

Hi, Brother Thank you for wonderful video. Please make a video, "How to add atoms in autodock parameter file". Because most of the metals are missing in autodock parameter file. For e.g I am facing a problem in preparing receptor file for pdb Id 1E9Z which contains Nickel items. When i add kollman charges, no charge were added to the nickel. Please let me know how to handle with the metals which are not available in parameter file of Autodock

[@vanshikarajsharma7314]

Wow, really insightful

[@Eternitypunklove]

THANK you for this!

[@jaannawaz2007]

Ur Welcome

[@shahnoushnayeri1240]

Hi. Many thank for your great description. but i couldnt find autogrid4.exe file. could you help me?

[@nhungdaothi719]

Thank you so much for your video. Can I ask some questions: 1. Do I need to optimize the ligand before docking? 2. How to redock with co-crystal?

[@Ricocase]

Cool video! Is fortran, c++, or python used to predict binding affinity and to what degree?

[@mungaimuiruri7607]

lets say i have one receptor/ and about 20 ligands, i am supposed to do this for each ligand? or one is enough

[@iqrasaleh]

sir, i could not find the autogrid4.exe and autodock4.exe files on internet? even your link is saying page not found? can you guide from where to get these exe files?

[@gutterball10]

I was able to successfully get up to time stamp @<a href="#" class="seekto" data-time="1472">24:32</a>. Upon trying to create the log file, something is going wrong. The log file will not generate in my parent folder. Not sure what is going wrong. Edit 1) Thanks for including the autogrid workaround @<a href="#" class="seekto" data-time="2005">33:25</a>. Edit 2) autogrid worked normally the second time I tried it through the regular program, I made sure there were no spaces or funny punctuation in any of the file names or folder names.

[@DMilannie]

Thank you very much for the tutorial, it was truly helpful! But I keep getting an error: insufficient grid points. /cygdrive/c/AutoDock/autodock4: WARNING: Unrecognized keyword in docking parameter file. /cygdrive/c/AutoDock/autodock4: ERROR: insufficient grid points. /cygdrive/c/AutoDock/autodock4: Aborting... /cygdrive/c/AutoDock/autodock4: Unsuccessful Completion. Could you please tell me how to avoid that? Thank you.

[@aravindnesaragi3980]

Very much pleased wid ua vid sir...really really helpful....I have a query sir, while selecting autogrid and after launch it is not going to run....can u plz suggest me a solution ...thank u

[@zohaibfayyaz7290]

i just want to know when you clicked on run autogrid and browsed program pathname from where autogrid4 application came from in that folder

[@yvonnesoki4825]

If I go to run autodock it starts and shows the little window for just a second and then nothing heppens anymore… No files are created but there is also no error showing up… What can I do?

[@divyarana3637]

Very clear sir. Thank you

[@chemistrywithharooniftikha3073]

Really appreciate your efforts. May Allah bless you.

[@naveennandu4213]

Hello sir, how should we get the executive files like autogrid 4. If anyone knows about that please explain

[@alchemist1979]

Hi When I Run finally autodock and click on launch It says in .dlg file that .C1.map file is missing What should I do

[@jingjingilove9500]

A very helpful guide for a beginner like me. Thank you so much sir. I can understand a lot better after watching this video. I would love it if you can make a tutorial on how to do a controlled covalent docking using Autodock 4 as well

[@jaannawaz2007]

So nice of you.. sure i will look on it

[@VikashKumar-cu4jj]

Good evening sir, I didn't found pdbqt format in openbabel GUI app. What should I do. Could you please answer my query it will be very thankful to you

[@saboor_saifi]

sir pls tell that how should i open .dlg and .glg file in word pad??

[@nikeshdewangan5247]

Sir, here I am facing one problem, the no.of torsion degree of freedom for my ligand is 36 I set it 32 to make some bond non rotable but when I was running the programs in last it sowing the no.of torsion is high .so sir please suggest me what should I do to overcome this problem?

[@lifesciencedecoded]

Sir which software is used to predict the anti-cancer compound ?

[@Crokai8]

I am trying to add Sn to the software but don't know how to do it, anyone could shed some light on the subject, please?

[@mahimasaraf7757]

Thank u sir but wanted to know at 24.36 autogrid4 come from where??

[@muhammadashraf1829]

Is there a video for the installation of Ubuntu, Perl and Autogrid ??

[@aimanparvez1409]

sir when i want to save the GPF then i get error and shows that you must select macromolecule before writing gpf

[@mariamaarof4646]

Thank you for the video

[@jaannawaz2007]

Ur most welcome

[@ExploreMalaya]

very informative ty sir

[@jaannawaz2007]

Ur welcome...

[@deepaknbotany166]

Sir after watching ur tutorial its very easy to perform docking work its simply superb sir but I have some error after step of run auto dock and I have not getting all other files after docking what I can do sir plz suggest me

[@mousegamersyt3398]

How can I download Autodock tool, Open Babel and VMD in one folder?

[@prabuddhabhattacharya3490]

Hi, thank you for this great tutorial. It is very lucid and informative. Can you kindly make a video on docking of transition metal complexes as ligand and metallozymes as the receptor protein? It will be very helpful.

[@jaannawaz2007]

Thanks for Watching... Yes, soon

[@SimranArora-hp5rq]

???

[@jaannawaz2007]

@SimranArora-hp5rq @plz send ur query to Dr’s email Address [e-mail]

[@SimranArora-hp5rq]

Ok

[@sazan447]

why did I miss the file it can't be created, I don't know where the mistakes will be glg file is missed what do I have to do?

[@tanyaralli3760]

Sir as I am choosing the macromolecule in grid, again and again it is showing list index out of range. Sir please help me how to correct it

[@ParveenKumar-cr2nc]

Phenol ki para position per bromine atom lagane pe mera cpd me bond nhi leta atom ke sath. Plz give me answer

[@surprisePharma]

Hello sir I am taking project on drugs design and chemistry but i have a lack knowledge what can i do for this.

[@dharanishreehk3775]

sir i got a error in python shell while building a missing residue in autodock

[@tulsivangari2727]

Thankyou..it was very helpful

[@shikhamudgal9418]

while using autodock4 command on linux terminal it is giving me following error: autodock4: FATAL ERROR: Sorry, I can't find or open AD4.1_bound.dat Please tell me how to resolve it?

[@aishasaddiqa3788]

hi. thank you for this valuable video. I have tried to run docking using your instruction. I have visualization problem in autodock. the line view of protein & ligand is clear but other views (ball & stick, surface, cartoon) are fade and grainy. can you please help me to solve this problem.. Thanks

[@jaannawaz2007]

visualization of docking complex.. Autodock is not a good tool, next video we will have docking results analysis... u can follow the same to create high quality publication images... Regarding the error, reinstall MGL tool software.. if still doesn't work... may be system doesn't have graphic card..

[@rabiyamehandi6354]

from where u save autogrid 4 to browse on <a href="#" class="seekto" data-time="1476">24:36</a> minutes sir

[@ogunoluwamayowa4749]

lovely tutorial

[@jaannawaz2007]

Thank U

[@chibakutensei6326]

Thank you sir. I have a problem after Run AutoDock, there is a statement "autodock4.exe: I'm sorry; I can't find or open "ligan" autodock4.exe: FATAL ERROR: autodock4.exe: I'm sorry; I can't find or open "ligan". How to solve this

[@apoorvalongtin]

Great information!

[@jaannawaz2007]

Thanks for watching!

[@melinaxupolutou6686]

does anyone know why autodock crashes after the selection of "add polar oxygens only" ?

[@TravelwithDebrup]

mentioned autogrid4 and autodoc4 downloading links are not working. Can you please mention a working link so that I can download those

[@pravallikadarru3333]

what to do when it shows error while repairing the atoms ? can somebody tel pls .

[@maliksaqibvs3811]

Sir if we want to do molecular docking, what will be your charge?

[@laxmisule7862]

when I am starting autodock, its showing "could not load module autoanalyze41 command" .... can anyone help me out

[@bitad]

Excuse me I don't have HD map form my atoms. Can someone tell me what is my problem?

[@shrirakshaa9166]

Hi, thank you for this well explained tutorial. I am facing this while ligand preparation- every time I try adding the ligand it shows an error that ligand.pdbqt cannot be read. Also, when checked, open babel shows a message that '0 molecules converted'. Tried numerous things but none worked out. Can I get any help on this?

[@knowledgeseeker9757]

convert sdf - mdl mol to pdbqt

[@Easypharmacy682]

Hello sir, mgltools not opened so how can i install it please tell me. I'm student

[@lifesciencedecoded]

Sir can we docked two target site for same disease by single ligand? Sir suppose x naam kaa ek ligand h jo A naam ke target site ko inhibit krra ho , phir suppose wahi x naam kaa ligand B naam ke target site ko inhibit krra ho, to sir kya hum ek saath A ligand ko dono target site(A and B) pe ek he saath docking kra skte h..... Multiple target site docking.... Sir plz doubt clear kar dijiye Agar kar sakte hain to kese ? Nahi kar sakte hain to kyu ni kr sakte?

[@hanstsahnang4533]

i love your video. this tutorial really helped thanks a lot, dear sir. can you do a tutorial on how to filter ligands during virtual screening campaign and how to validate a virtual screening protocol. thanks

[@jaannawaz2007]

u can check this video kzbin.info/www/bejne/qnepqYGKq9uigKs

[@sumitmallick7951]

thanks for this video. I have a question. How i will delete hetero atoms ad prepare protein for final docking?

[@jaannawaz2007]

i already shown in video

[@harievignesh7252]

Sir, how to take the average value for setting up the gridbox if the pdb co-ordinates come in both positive and negative signs?

[@gutterball10]

Think back to basic math. Include the sign when taking the sum. This assumes the Cartesian grid origin is somewhere in the middle of the receptor, as apposed to the entire receptor getting displayed in 1 quadrant or octant of the 3D grid.

[@phdmastery1775]

Thank you for the great tutorial. This was very helpful! However, I get an error at the last docking step which does not continue. It shows me the message: WARNING: Unrecognized keyword in docking parameter file. Thanks for your help.

[@jaannawaz2007]

Try again

[@maharshidixit3183]

Hello, This video really helped me start well. Thank you for that. But I'm facing an error while repairing the missing atoms. I have 994 missing atoms, and it shows "tclerror: no more menus to be allocated" midway while repairing. What should I do? Thank you.

[@bibaswanbiswas1583]

me too. have you fixed this>

[@younessmoukhliss5593]

Hi all, thank you very much for your efforts. when the ligand is inserted, it is placed away from the active site. how can this problem be solved? thank you very much.

[@jaannawaz2007]

increase the population size, and increase the grid box size..

[@insight_excursion]

Where did we get the autogrid4

[@muhammadashrafhadirosman3845]

do you have toturial in using aptasuite

[@stan9095]

When pasting into OpenBable GUI, make sure that the input format is selected as sdf - - MDL MOl format. My ligand file would not convert to .pdbqt until I made this change.

[@jaannawaz2007]

Open Banel GUI having multiple options ... check input file format correctly

[@parimalakopalle7639]

Hello sir.. You have explained everything very clearly. It was very informative and easy to understand. I just wanted to ask the fourth amino acid which you selected was Lysine (270) and in the excel sheet it was given for Serine. Please clarify.

[@obasajuwinner215]

Yes, i saw that as well. I guess it was a mistake, he should have selected Ser272

[@nirmalthirunavookarasu9749]

Sir, the best combination for autodock is 50 GA run and 300 population size only or can we increase it further. If we didn't change GA number of evaluation in accordance with number of torssions will it affect our docking?

[@gutterball10]

I think there is a tradeoff between increments and compute time. The larger your population sizes and GA increments, the longer it will take to compute. I suspect these values are chosen to offer a balance between accuracy/precision and a reasonable compute time on a standard computer. If you have a more powerful computer you can probably turn these settings up.

[@nakulbhardwaj3777]

Sir, thanks for such an informative video! I just want to ask if our ligand is away form the protein or receptor then what should we do?

[@abeerahassan1847]

Same question. Does the program automatically place the ligand in the binding pocket once it is loaded?

[@ashrafwazir5037]

Thank you for uploading such an excellent presentation.. Kindly if possible upload video about metal docking in ligand and how to prepare paramter file for metal. Thanks regards

[@jaannawaz2007]

Sure coming soon.. u can check my published articles.. u will find a tool for metal docking

[@ashrafwazir5037]

Thank you for your kind response.. most of the bioinformatics and related field students wait for your tutorials.. please if possible kindly provide the link of the metal docking paper.