Molecular docking for Beginners | Autodock Full Tutorial | Bioinformatics
ฝัง
- เผยแพร่เมื่อ 26 ก.ย. 2024
- 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.scripp...
Autogrid4 and Autdock4 : autodock.scripp...
Open Babel GUI: github.com/ope...
Literature:
www.ncbi.nlm.n...
autodock.scripp...
www.sciencedir...
I went through your presentation sir and I was able to understand it. Thank you very much. We plead for more like this.
Ur welcome
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
This video will stand as a landmark in my future studies on docking. Well done and Thank you.
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 ❤️
hi i am facing python shell error please help me in rectifying it
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!
Thank you so much for tutorial. It was very useful for beginner and even non biology majors also understood clearly.
Glad it was helpful!
Amazingly clear tutorial! Finally got autodock working!! Thank you so much!
Wonderfully curated Video Sir. From the start, till the endpoint I was able to keep up as exactly as you were demonstrating. Please continue to make such videos which makes our learning clear smooth and effective for future applications
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.
Thanks For Watching... Soon we will
Really good tutorial, not just what to do but also why. Thanks!
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?
what is the best docking tool for peptide interactions with protein or protein-protein interactions
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
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?
Hello sir I am taking project on drugs design and chemistry but i have a lack knowledge what can i do for this.
Many thanks for wonderful presentation.
When I read a paper about andrographolide as a potential inhibitor of SARS-CoV-2 main protease: an in silico approach. The andrographolide compound has a free energy of -3.09 Kcal/mol, but it shows great binding when compared to other compounds having more negative free energy values. I think about pressure, temperature, and pH in the body affecting the inhibitory process
Indeed, this variable influences the inhibitory process; it is advisable to do molecular dynamics calculations to complete the molecular docking calculations.
Hello sir, how should we get the executive files like autogrid 4. If anyone knows about that please explain
Hi. Many thank for your great description. but i couldnt find autogrid4.exe file. could you help me?
Very hlpful and thankyou sir! Can you please tell where to get the executable files (autogrid4 and autodock4)
Hi, hope it will help you - i found them occasionally after autodock installation in C:\Program Files (x86)\The Scripps Research Institute\Autodock\4.2.6
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
So nice of you.. sure i will look on it
Hello Sir, in Openbabel I selected the sdf - - MDL MOL format to upload my 2D ligand but in output the pdbqt format is not displayed. There is just pdb format. My ligand is simply a cadmium ion and the protein is IVQQ present in Streptococcus pneumoniae. If I convert sdf to pdb format the ligand file is not getting opened in Autodock. To which format should I convert the ligand sir? Thank you
I was able to successfully get up to time stamp @24:32. 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 @33:25.
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.
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.
Open Banel GUI having multiple options ... check input file format correctly
Thank you very much. So helpful video
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
Sure coming soon.. u can check my published articles.. u will find a tool for metal docking
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.
Hi
thank you very much for your video.
I'm trying to dock but I can't do it because I get an error that says: Sorry, I can't find or open Grid Parameter File. I checked your video and I have everything the same, I don't know what the cause of the problem would be. I created a folder in documents which contains the files and also the executables for autodock4 and autogrid4; executables that were initially found in a folder called: The Scripps Research Institute located at C: \ Program Files (x86). I have tried to do several maneuvers but I cannot start the program. Thank you, if it is the case, help me with this difficulty.
share ur error screenshot in our Bionforamtics facebook group
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.
Yes, i saw that as well. I guess it was a mistake, he should have selected Ser272
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?
sir when i want to save the GPF then i get error and shows that you must select macromolecule before writing gpf
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
u can check this video th-cam.com/video/tFFxNTvvoJI/w-d-xo.html
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?
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?
from where these application "autodoc4 , autogrid4" we will get ? i mean inside MGL Tools i can not see anything named it. could you please help what exactly i need to have in the working directory.
Thank you for the video. How do you dock two proteins? Not protein and ligand
Very useful and easy to follow, Thank you
Phenol ki para position per bromine atom lagane pe mera cpd me bond nhi leta atom ke sath. Plz give me answer
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?
Same question. Does the program automatically place the ligand in the binding pocket once it is loaded?
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.?
Small doubt @13:20. In this tutorial you have added only "polar hydrogens" to the protein structure, but in autodock tutorial it is mentioned to add "all Hydrogen" - So whatis teh difference bewteen these 2 ? How adding all Hydrogens or polar only hydrogen affect the docking result ?
try running an experiment comparing the results when the two different options are used and see what happens. Perhaps this relates to giving preference to hydrogen bonding over a balanced consideration with hydrophobic interactions included. I'd be willing to bet incorrect results will occur if only polar hydrogens are used in the simulation when hydrophobic interactions are important for binding.
sir if a person gets a large positive value with my protein somewhere around 2856kcal/mol. In autodock vina i received a normal binding energy of -10.1 kcal/mol with the same target and ligand. What could have gone wrong according to you?
ur question is not clear to me. if ur talking about protein-protein docking, yes u will get highest docking energy values, b'c there are many residues are involved in interaction for that reason u will get many h-bonds, vdw, ioinic interaction etc., but when it's come to small molecule u will find very minimal interactions.
With vina and Autodock, i m getting very different results.
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.
Thanks for Watching... Yes, soon
???
@SimranArora-hp5rq @plz send ur query to Dr’s email Address bbabajan@kau.edu.sa
Ok
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
sir Apart from ligand and macromolecule you have another autogrid and autodock file. kindly tell me where i can get those files
Hi! I have the same question like u, so do u know how to have that files? Can u help me? Thanks
Would also like to know that
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
finally i got my output with your tutorial, thank you sir... but i haven't get any rmd table in dlg file and i have get no more hydrogen bonds are created in analyzing conformations, may i know the reason sir and please tell me how to rectify it
Hi thank you for good video ! I want to ask, what if we put xyz randomly as long as the ligan in the cube ?
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
Thank you for sharing very useful information.
I am facing a problem when I repair my protein molecule for missing atoms. The program got stuck and do not further process. What should I do about this?
same issue with me, it is showing python shell, errors, how to resolve please help
@@JaspreetKaur-ry2nbReinstall the MGL tools and python and use latest setups for both
lets say i have one receptor/ and about 20 ligands, i am supposed to do this for each ligand? or one is enough
Really appreciate your efforts. May Allah bless you.
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 ?
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.
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?
I am very happy to understand all these very clearly but there is a problem facing when I am doing docking of my derivative plz you can help me
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
Thanks for video, could you please tell me, in my case why it shows error "receptor.maps.fald"?
hello sir, first of all i would like to thank you for this awesome tutorial,but sir i have problem while saving gpf file , it is showing "you must choose a macromolecule before writing gpf"
I also have same question
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
Thank you for the video
Ur most welcome
Sir , what if the ligand is not inserted to the protein
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?
i just want to know when you clicked on run autogrid and browsed program pathname from where autogrid4 application came from in that folder
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
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.
Cool video! Is fortran, c++, or python used to predict binding affinity and to what degree?
Autogrid is not running and glg file is also not generated any solution. please help
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?
I'm getting an error during running autogrid4, it's not running.
sir please share the link of autodock4 autogrid 4.. the link is not working
From where autogrid4 comes, I'm confused
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?
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
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?
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 :(
Excuse me I don't have HD map form my atoms. Can someone tell me what is my problem?
Hello sir, mgltools not opened so how can i install it please tell me. I'm student
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?
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?
How did you get the amino acid in the PyMol ? Can you show this?
Sir which software is used to predict the anti-cancer compound ?
Good job! I really liked the tutorial. grateful.
Glad you enjoyed it!
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?
convert
sdf - mdl mol to pdbqt
mentioned autogrid4 and autodoc4 downloading links are not working. Can you please mention a working link so that I can download those
How can I download Autodock tool, Open Babel and VMD in one folder?
Very clear sir. Thank you
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.
does anyone know why autodock crashes after the selection of "add polar oxygens only" ?
Sir one request : plz suggest some list of good laptops for doing molecular docking project!!!🙏🏻🙏🏻🙏🏻
Thank u sir but wanted to know at 24.36 autogrid4 come from where??
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.
me too. have you fixed this>
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
what to do when it shows error while repairing the atoms ? can somebody tel pls .
Sir I'm facing error after selecting grid>macromolecules>choose>select molecule and then error can you please help me 16:43
It is very very good! Thank you for work!!!
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
I followed all steps throughly but docking is not starting. I getting a message "can't find or open grid parameter file" can you tell me what went wrong?
check the parent directory and make sure that all the file types are present. When I tried working through this tutorial, the log file was not generating, and I couldn't run the simulation.
thank you very much, but I need to list the steps, and how about simulation, I docked O6K to covid 19 protein, but after repairing the missed atoms, the auto deck Vina stopped and did not work, after I made docking how can I go to Gromacs for simulations .
also, covid 19 protein has 2 chains, I must do docking for the two chains or only one, you must know that after removing the heteroatoms and repairing the missed atoms, I saw that O6K returned to the structure.
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
Is there a video for the installation of Ubuntu, Perl and Autogrid ??
when I am starting autodock, its showing "could not load module autoanalyze41 command" .... can anyone help me out