Molecular Docking | Autodock VINA Virtual Screening | VINA Docking tutorial | Bioinformatics

Virtual screening based on molecular docking is becoming a powerful tool in identifying lead compounds in a huge pool of small molecules.After the construction of library and preparation of receptor, each compound in the library is virtually docked into the target binding site with a docking program.
The Docking aims to predict the ligand-protein complex structure by exploring the conformational space of the ligands within the binding site of the protein. A scoring function is then utilized to calculate the free energy of binding between the protein and the ligand in each docking pose or confirmation. Docking and scoring produce ranked compounds, which are then post-processed by examining calculated binding scores, validity of generated pose, undesirable chemical moieties, metabolic liabilities, desired physicochemical properties, lead-likeness, and chemical diversity.
Post-processing results can filer down the compounds, which can be further proceed to experimental assay to identify potential compounds.
AutoDock Vina significantly improves the average accuracy of the binding mode predictions compared to AutoDock 4.
MGL Tools: mgltools.scripps.edu/
Autodock Vina: vina.scripps.edu/index.html
OpenBabel: bit.ly/3eMgXZm
Perl: padre.perlide.org/
PerlScript File: bit.ly/31gNgef
Literature:
www.nature.com/articles/s4159...
pubmed.ncbi.nlm.nih.gov/28809...
experiments.springernature.co...

[@mollylu3638]

Thank you this has been VERY VERY helpful and I really appreciate your tutorial. Everything is so clear and I love how you also provided sources on where to find downloads :)

[@DanielLopez-uf7dw]

You just saved my undergraduate thesis research. Thank you so much!!

[@robertobellomadruga2732]

Thank you very much. It is an excellent tutorial for virtual screening in Autodock Vina

[@govindajadhav1666]

It's an excellent tutorial for virtual screening using autodock vina

[@MARIALUIZAPEREIRABALTAZAR]

This was SO MUCH helpful!! Thank you for the amazing explanation!

[@sportnrelaxmoments7275]

Great job, Thank you so much Professor.

[@architakhaire5313]

Thank you! How do I add new atom types in Vina, specifically for Silicon? Is there a parameter file like GPF or DPF that needs to be edited?

[@zainonesaabrahams-october2214]

Thank you this was very informative and easy to follow. Much appreciated.

[@jaannawaz2007]

Glad it was helpful!

[@user-gj2cl2rr9x]

Thank you so much for the video. I have a little question about the small peptide as ligands. when I transform it from pdb file into pdbqt file. it was broken (when i visualize them by chimera X or pymol). Do you have any solution for the transformation ?

[@jakstat9880]

Youre amazing. Thank you so much.

[@zyx6239]

This video tutorial is truly helpful for my thesis. I have a question though... Why is the exhaustiveness parameter is not typed out in the configuration file or Vina will carry it out at default ?

[@arosh2094]

Thank you sir for this wonderful guidance !

[@MuzzammelRehman]

kzbin.info/www/bejne/i2W7mZKMfdhjf6c

[@_lemonny]

Wonderful tutorial! This will save me a lot of time (8 protein targets and 23 ligands). I was going to be very selective about the ligands, but I don't have to be now.

[@preetimahra8679]

@Thomas Lemon Hello sir, could you please tell me how did you do that (8 protein target and 23 ligands) at a time. Have you dock one protein with 23 ligand and again another protein with 23 ligand and so on?

[@_lemonny]

@@preetimahra8679 I ran a total of 8 scripts, one for each protein.

[@preetimahra8679]

@@_lemonny Ok, Thank you.

[@jameelabduljalil25]

Hello Sir I hope you are doing great I have tried to use the perl script with the new version of Vina (v 1.2.3) but Vina didn't recognize the --log argument in the script. Is there any problem/modification?

[@ashrafwazir5037]

This is another master piece from you sir. Kindly add tutorials about ligand DNA docking using autodock. Thanks regards

[@jaannawaz2007]

Noted

[@athirat4021]

Thank you so much, this is very informative and help me a lot in doing Autodock

[@athirat4021]

I got an error after running the script for docking, but I get the results as log and out files. Is this error message affect the result? "Command line parse error: too many positional options"

[@Zack6ix]

thank you for this, is this still the easiest way to use autodock vina for screening a library of ligands?

[@tjroxas1322]

Hi, where can I find the citation for the Perl script? Thanks a lot!

[@AsifRaza-oq4nb]

Sir, what does the other two columns mean in the out_log file?

[@SureshKumar-ef8xu]

Sir , can you please tell me how to do energy minimisation for protein and ligand. Can you post video on result analysis by using pymol software.thank you

[@tonz1956]

this tutorial is very helpful in my thesis!! i want to add it in citation. which journals can I cite?

[@user-oh9zk7cb6m]

Thanks for your lectures Sir Can you please explain the steps of ( metal complex) docking??

[@asif4557]

do we need to add charges for ligand ? like protein

[@armintoghi6769]

hey sir, why don't we just use Pyrx ? is there any difference with accuracy or sth else?

[@AmalAli-uv7lh]

Is there a script that can help us rank the output files according to the best energies?

[@W_T24]

thank you its was really clair

[@Toisssoo]

very informative, greeting from brazil

[@jaannawaz2007]

Thank You so much

[@KalaniK2315]

Hello I have been having issues with the autodock reading my ligand file. I used the .pdb format, but the program keeps giving me an error message when I input it. Is there a way to fix that?

[@gunjanlakhanpal2390]

Thankyou! I am getting an error "IndexError: list index out of range" while choosing the macromolecule. Plz help me with this.

[@camilla532]

Thank you so much for this helpful tutorial! I am having an issue if I can ask. When I run the command, the cmd says that access is denied.

[@rohitchel5679]

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?

[@mylam1605]

Thank you for your informative video, sir! I followed those steps but I got error: "Can't open perl script "Vina_windows.pl": No such file or directory". Can you help me?

[@josepramoncodinagarcia-and8162]

Thank you for your work. What software would you recommend to generate 3D conformation of molecules?

[@namnhathoang6858]

winmostar

[@Scienceforall2020]

hi the video was very informative, but after running the perl . I got this message. WARNING: The search space volume > 27000 Angstrom^3 (See FAQ) Output will be ligand_out.pdbqt Detected 8 CPUs Reading input ... done. Setting up the scoring function ... done. Analyzing the binding site ... Error: insufficient memory! but there is more than 500 gb available in C drive? any help with this?

[@gutterball10]

What is the purpose of the step taken @9:10, changing the histidine hydrogens?

[@aluisiomarquesdafonseca5901]

Dear I would like to know if it would be possible, within the script, it run the vina_split? for poses.... or organize into separate folders?

[@jaannawaz2007]

no i didn't tried to embed split command, but its easy to run split command in a shell after docking. vina_split --input output.pdqt

[@RahulGupta-nf8ke]

Great effort BB!! Keep up the good work... can you please tell me what is your system configuration? like RAM, Processor etc. I am just starting with bioinformatics and your advise will be of much help.

[@jaannawaz2007]

This my System Configuration : Lenovo Legion Y740 9th Gen Intel Core i7 15.6 inch FHD Gaming Laptop (32GB RAM/2TB SSD/NVIDIA RTX 2060 8GB Graphics

[@SvaraMandira]

Can you show us how to dock between DNA and protein, unable to get a secondary structured DNA in PDB format.

[@mrfurious9975]

hello sir can we converted sdf into pdbqt file and run in autodock vina easy

[@prddeep]

Thank you sir for your guide but after doing it all i am not able to get dlg(data log file) in data folder as you show in "autodock result analysis" video..so please guide us for it.

[@jaannawaz2007]

if u have carefully done the above tutorial.. i am sure u will sure u will get log file at the end.. if u still getting error.. u can post ur error screenshot in our facebook page facebook.com/groups/261045198486665

[@afsaralam2385]

Now we have instadock which have very easy graphical user interface and very easy to use and runs on autodock vina

[@Rahulraj-kp1eu]

Is there any special reason for downloading ligands as separate files instead of single *.sdf file.

[@MuzzammelRehman]

Multiple Ligand Docking by Autodock Vina through command line in UNIX/LINUX

[@MuzzammelRehman]

kzbin.info/www/bejne/i2W7mZKMfdhjf6c

[@karimbarakat3681]

Great video, Thanks alot and this the best lecture in docking that i have ever seen. but my question: What is the purpose of the step taken @9:10, changing the histidine hydrogens? why not +1? and why you didnt apply force field for the compounds?

[@tejalkhanna15]

I followed all the steps,but it's showing " parse error on line 2 in file " in my ligand pdbqt file? Please help

[@diosyahputra838]

What is energy range stands for?

[@blister981]

This works.Thankyou . Is there any way to run this program in google colab???

[@computational_biophysics]

Thanks for this video. Could you tell me how did you convert the 100 files from .sdf to .pdbqt? did you do it one by one or there is a script? thanks

[@jaannawaz2007]

Bioinformatics With BB 3 weeks ago Your welcome... Regarding your question, you can't convert directly smile format to pdbqt, initially u have to convert into pdb file and from pdb u have to convert into PDBQT. 1. smile to pdbqt (Open Babel or you can use smile converter online tool check > u can upload multiple smile in text format cactus.nci.nih.gov/translate/) 2. pdb to pdqt (Open Babel or Racoon plugin > check this link www.researchgate.net/post/How_can_you_convert_a_large_number_of_pdb_files_to_pdbqt_files) if you any other concerns you can post ur question in our facebook group page facebook.com/groups/261045198486665

[@computational_biophysics]

@@jaannawaz2007 thank you for your help

[@jameelabduljalil25]

Do ligands need not to be minimized or some kind of processing prior VS?

[@MuzzammelRehman]

kzbin.info/www/bejne/i2W7mZKMfdhjf6c

[@snehakushwaha5177]

Sir prepared all files, facing error Phrase error in line all the ligand pdbqt files unexpected multi-MODEL input Use "vina_split" first? getting this error pls solve

[@ismaildin69]

Very interesting and informative video kindly can anyone of you can help me. Thanks

[@abdulmalikaliyu8876]

Thank you for all the tutorials, sir. I tried to run Autodock Virtual Screening and each time I run the "repair missing atom" it will not complete as in your previous tutorial, it will stop running, the program will hang and I will not be able to proceed. Please, how do I go about it, sir?

[@jaannawaz2007]

if repair missing atom is having issue with u, u can rebuild the model in swissmodel server.. after building the model, u can skip the repair missing atoms step in audotock

[@anumnaz6665]

same thing happens with me

[@user-wy2ud3rx9j]

@@jaannawaz2007 could you make video on that, if possible

[@azeezishola2912]

Good day. Please is there any command code to do multiple scoring of different compounds in autodock vina. thanks

[@jaannawaz2007]

Check my next video on VINA

[@murtazagmg]

Very informative. Can you guide how to perform autodock vina for large ligands e.g. DNA?

[@MuzzammelRehman]

kzbin.info/www/bejne/i2W7mZKMfdhjf6c

[@duasaleem3677]

Sir I have downloaded perl in my laptop but still command prompt don't recognize it kindly guide me in this regards

[@jaygagare4333]

I also have same problem, do ur problem solved?

[@pratiklonkar1057]

I followed all steps but I got error "Configuration file parse error: unknown option num_mod" now what to do pls help

[@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?

[@snehakushwaha5177]

It can be done, as we do in blind docking, make grid of both these two pockets, and then perform docking

[@chiragsoni6770]

Can i use this tool for publication? And what's the reference of this tool bcz i have to do mention it in paper.

[@jaannawaz2007]

Refer this book.. www.amazon.com/Bioinformatics-Biomedical-Discoveries-Mathematical-Computational/dp/1498724523

[@newdiscovery665]

How to rank a list of solutions (i.e 1000 compounds = 1000 log files) from autodock Vina? Do you have some script or method to rank for the best solution (compound) from such a list of log or PDBQT files from Vina? Thank you in advance.

[@jaannawaz2007]

iam working on it, next video u will see complete script

[@murshadahmed3411]

U should try vstop.py script

[@danishiqbal7774]

​@@jaannawaz2007 dear BB, could you please share the video link for this next video you mentioned to get the results of binding energies in one file because i am using big database and I need all the results in one excel sheet as usually obtained in PyRx tool. I tried to use PyRx tool for my dataset but all time I got some parse error showing that atom are missing in ligand. Vina is working fine but the only issue that I need all the results of binding energy in one single file to analyze easily

[@anshikagupta4301]

Thanku sir for very much informative session..i want all binding energy of complex in one notepad file then how can i do this?? Please if you can help because i have huge number of ligands and it is not possible to open one by one file.

[@teuzen7900]

Please I need an answer to this problem too

[@anshikagupta4301]

@@teuzen7900 he has already given the answer to this problem in his next video please do check

[@debasishpattnaik5921]

Sir I am interested in learning bioinformatics. What basics I should know. I know basic biotechnology and biochemistry but when it come to softwares tools I am confused. What are the programming language I should start with. It will be very helpful if you can make a step by step things to learn for a beginner like me to excel in bioinformatics field.

[@jaannawaz2007]

There is two options, one is software developer, requires advanced programming skills, second one is data analyst, require less programming skills. The choice is totally depends upon what's ur background area.. if ur not familiar with programming my suggestion is go with option 2, its really hard to develop programming skills in short period.

[@oktavialisti172]

to convert ligand file using open Babel GUI, should we convert one by one or can we upload all ligand in the folder and they will convert all of the ligand automatically?

[@MuzzammelRehman]

kzbin.info/www/bejne/i2W7mZKMfdhjf6c

[@MuzzammelRehman]

I have converted the ligands in open babel in the video in provided link

[@oktavialisti172]

Thank you for your response

[@ila_1910]

after giving the command, perl vina_docking.pl it writes perl is not recognised as internal or external command, operable program or batch file. What may be the reason for this.

[@MuzzammelRehman]

kzbin.info/www/bejne/i2W7mZKMfdhjf6c

[@lifesciencedecoded]

Sir jese hum docking karte time receptor protein kaa interaction karte hain , us time receptor protein kaa water remove karte hain, or ligand kaa interaction karte hain, but natural condition main recepror protein main water rahega, phir interaction kese hoga..... Sir plz doubt clear kar dijiye .... Usually water active site ko distort krta h interaction ke time, tbhi hum water molecules ko remove karte hain , but jab hum koi medicine/ligand create kar lenge to wo to phir body ke inside receptor protein main water hone se interaction hi nahi hone dega natural condition main..... Plz clear the doubt of my question sir .....

[@MuzzammelRehman]

kzbin.info/www/bejne/i2W7mZKMfdhjf6c

[@dsnbk]

Error is coming like could not open "conf_vs.txt" for reading. Please help me out

[@70pradeepyadav5]

After this step, how to get 2D interactions?

[@guglielmomontarani5048]

Can you please make a video in which is explained how adding a metal ion ?

[@jaannawaz2007]

sooon

[@spider4957]

❤❤❤❤❤

[@sofianehocine499]

In autodock vina the spacing parameter suppose to be at 1 in the gridbox panel

[@user-tw9zn7vy2l]

I think you are right, but why no one noticed that in this video?

[@sofianehocine499]

@@user-tw9zn7vy2lit is in the manual 🤷🤷

[@jsj485]

Openbabel 3.1.1 doesn't offer pdbqt format. When Pymol read lots of sdf or mol2, it doesn't work well with error. How can I convert lots of sdf or mol2 into pdbqt?

[@MuzzammelRehman]

kzbin.info/www/bejne/i2W7mZKMfdhjf6c

[@MuzzammelRehman]

check the conversion in this video

[@manojdhameja4212]

Thanks sir. After performing docking of single ligand, i m getting error "insufficient memory". My pc has 6gb ram. What to do now ? Please help

[@jaannawaz2007]

need to work on workstations or u need to increase the specs of ur computers

[@manojdhameja4212]

Thanks sir, i m able to perform the same. I ve a query. What is the meaning and significance of 0,HD1 0,HE2 and +1 in Edit Histidine Hydrogen dialogue box ?

[@manojdhameja4212]

In my protein, 0,HD1 is already been selected. Should I select 0,HE2 (as you did) ?

[@manojdhameja4212]

Sir please reply #Bioinformatics With BB

[@vijaynirusimhan6151]

1. Will you sahre the script file to run virtual screening? 2. Shed some light on how write the ligands name in ligands.txt file using "command"

[@jaannawaz2007]

check in the description box

[@shwetapotdar6480]

Sir please make a video on DFT studies too pls sir 🙏

[@tanishkamehta2612]

I have perl error when I put perl in command

[@flyhigh6561]

Very informative.. sir where did you give that pearl script file ? Can you please provide that..

[@jaannawaz2007]

Check in Description Box

[@flyhigh6561]

Thank you sir

[@amanyassem7816]

Thanks for your excellent video, I have an error could anyone help me?! It Is warning: couldn't find any conformations completely within the search space Warning: check that it is larger enough for all movable atoms, including those in the flexible side chains

[@kirk0831]

omg, so you need to manually click 100 times to convert sdf to pdbqt one by one??

[@jaannawaz2007]

1. smile to pdbqt (Open Babel or you can use smile converter online tool check > u can upload multiple smile in text format cactus.nci.nih.gov/translate/) 2. pdb to pdqt (Open Babel or Racoon plugin > check this link www.researchgate.net/post/How_can_you_convert_a_large_number_of_pdb_files_to_pdbqt_files) if you any other concerns you can post ur question in our facebook group page facebook.com/groups/261045198486665

[@jaannawaz2007]

1. smile to pdbqt (Open Babel or you can use smile converter online tool check > u can upload multiple smile in text format cactus.nci.nih.gov/translate/) 2. pdb to pdqt (Open Babel or Racoon plugin > check this link www.researchgate.net/post/How_can_you_convert_a_large_number_of_pdb_files_to_pdbqt_files) if you any other concerns you can post ur question in our facebook group page facebook.com/groups/261045198486665

[@rajanrolta4832]

hello sir iam getting a problem with the last step my confg_vs.txt file is not opening it showing an error please help me

[@MuzzammelRehman]

kzbin.info/www/bejne/i2W7mZKMfdhjf6c

[@abdulashikkhan5912]

Please give an example with metal docking

[@md.mahfuzurrahmanbhuyan9351]

Sir, How many nodes do i need for research?

[@MuzzammelRehman]

kzbin.info/www/bejne/i2W7mZKMfdhjf6c

[@rajeshrajesh-xc2fo]

Hello sir, I can't complete the docking process it shows "Command line parse error: too many positional options" How to fix this error? Thanks Warm regards Rajesh

[@azeezishola2912]

Good day. I experienced similar error too. I fixed it by renaming my config.txt file to "conf_vs.txt". Try and do same to see if fixed

[@jaannawaz2007]

Try again

[@jaannawaz2007]

post ur query in our facebook page facebook.com/groups/261045198486665

[@MuzzammelRehman]

kzbin.info/www/bejne/i2W7mZKMfdhjf6c

[@robertsonrivera9775]

baba jan how to prepare multiple ligands all at once? thank you!

[@sailendramahanta2213]

C:\>cd "Vina Docking">dir /B > Ligand.txt Access is denied. Stuck here. Can you help me out..

[@MuzzammelRehman]

kzbin.info/www/bejne/i2W7mZKMfdhjf6c

[@anujpiash8749]

sir, why the script link is not working??

[@MuzzammelRehman]

kzbin.info/www/bejne/i2W7mZKMfdhjf6c

[@goranpani8438]

Very informative, can we get that pearl script file please

[@jaannawaz2007]

Check in Description Box

[@anshikagupta4301]

Thank you very much sir sir this is very useful for me ...i was searching script for multiple docking using vina since many days but today i found this on your channel this is the best tutorial i have ever seen... Sir actually i want to convert csv file of smiles into pdbqt ...how to do it ? Please if you can help .

[@jaannawaz2007]

Your welcome... Subscribe to our channel to get more interactive contents in Bioinformatics. Regarding your question, you can't convert directly smile format to pdbqt, initially u have to convert into pdb file and from pdb u have to convert into PDBQT. 1. smile to pdbqt (Open Babel or you can use smile converter online tool check > u can upload multiple smile in text format cactus.nci.nih.gov/translate/) 2. pdb to pdqt (Open Babel or Racoon plugin > check this link www.researchgate.net/post/How_can_you_convert_a_large_number_of_pdb_files_to_pdbqt_files) if you any other concerns you can post ur question in our facebook group page facebook.com/groups/261045198486665

[@anshikagupta4301]

Thank you !🙂

[@xyz-vz9iy]

Script file did not work in Linux could you provide the same for linux

[@xyz-vz9iy]

this is the error: sh Vina_windows.pl Vina_windows.pl: line 2: printLigand_file:\t: command not found Vina_windows.pl: line 2: $' ': command not found Vina_windows.pl: line 3: syntax error near unexpected token `;' 'ina_windows.pl: line 3: `$ligfile=;

[@user-wc8ys3uo2b]

Hii sir, I am facing this type ofproblem ....pls help me lig_9.pdbqt Configuration file parse error: unknown option centre_x Correct usage: Input: --receptor arg rigid part of the receptor (PDBQT) --flex arg flexible side chains, if any (PDBQT) --ligand arg ligand (PDBQT) Search space (required): --center_x arg X coordinate of the center --center_y arg Y coordinate of the center --center_z arg Z coordinate of the center --size_x arg size in the X dimension (Angstroms) --size_y arg size in the Y dimension (Angstroms) --size_z arg size in the Z dimension (Angstroms) Output (optional): --out arg output models (PDBQT), the default is chosen based on the ligand file name --log arg optionally, write log file Misc (optional): --cpu arg the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1) --seed arg explicit random seed --exhaustiveness arg (=8) exhaustiveness of the global search (roughly proportional to time): 1+ --num_modes arg (=9) maximum number of binding modes to generate --energy_range arg (=3) maximum energy difference between the best binding mode and the worst one displayed (kcal/mol) Configuration file (optional): --config arg the above options can be put here Information (optional): --help display usage summary --help_advanced display usage summary with advanced options --version display program version

[@aishasaddiqa3788]

from where I download script file?

[@jaannawaz2007]

Check in Description Box

[@devildead470]

8:30

[@VikasKumar-bn6rf]

Very informative..do I get your mail ID?

[@MuzzammelRehman]

kzbin.info/www/bejne/i2W7mZKMfdhjf6c

[@sderese]

The problem with Autodock vina is the errors

[@MuzzammelRehman]

kzbin.info/www/bejne/i2W7mZKMfdhjf6c

[@zaenalwatoni2488]

this tutorial is very helpful in my thesis!! i want to add it in citation. which journals can I cite?

[@Ray4rafia]

Hey, Have you published any paper related to this ? If yes then kindly send link