Please do keep making this type of videos it's very helpful

The best video on KZfaq... thank you very much sir

That is an excellent video. I'm really really thanks for it.be a successful and happy, dear doctor

Thank you so much dear BB, I raised my query in previous video and got my answer from this current video. Now it will be very easy to analyze the results.

Thank you ❤️ for making this video it solved my doubts about docking multiple ligands.

Thankyou very much , it was so useful

sir, can you tell which scoring is used in this method, AutoDock 4 or Vian scoring function?

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?

Hello, thanks a lot for the video. I got one issue with my rankings. When I dock 500 molecules in my VS set, and I need to sort all docked molecules by the number. I end up having ~20 molecules with same score..because Autodock provides only 1 decimal number. How do I know among 20 which one is ranked better than the other etc?

Sir how we can dock a rigid protein and multiple flexible proteins at once. Waiting for your reply.

@23:31, Having an issue with executing the "perl" command in ubuntu. It's not following up with the yes or no prompt, the following lines are just blank.

Very informative video! But i have one query. While converting .pdb files to .pdbqt files using obabel command, most of the hydrogens are missing along with some other heteroatoms. But when i convert them using autodock tools, its working perfectly. Is there any way to convert them using autodock tools with just one command? Please help. Thank you.

Thankyou for this tutorial, I was wondering if you can make tutorial on the updated VIna 1.2.3 version with latest features it is offering

Thanku so much again for this wonderful session.

Really a very informative video. Each step clearly explained and worked for me sir. I am a researcher from amity university. How can we cite this work in our paper? Also sir, what does adding kolmann and gastegiers charges means?? I didn't added any one of them!! Plus sir, is making model of protein compulsory. I read somewhere on RG that of protein is having good resolution then missing residues are least.

Worked😄Thank you so much!!!

Thanks a lot, these videos always really help. Interestingly, I can't find a good tutorial for docking two ligands at the same time: A heme group, and an enzyme substrate for p450. This is different than what most people ask. It seems most people want to try many ligands to see which one is the "best". What I would like to do is take my p450, dock it first with a heme group, then dock the whole structure (p450 + heme) and dock it to a ligand. I managed to dock the heme group alone to my p450 using autodock vina in UCSF Chimera. But when I run docking simulations, I am only allowed to choose one receptor (either the heme, or the p450). The obvious problem is that autodock vina then attempts to dock the ligand to the p450 while ignoring the heme group. Any advice on this? Thanks!

Thank you for the tutorial, can we just choose the repair the missing atom in the autodock tools options instead of build model from PASTA sequence for repairing the missing atoms?

Thank you for the freat video. what do you do if you have multiple ligands and multiple receptors? would you please share the script? Thank you

Hello sir , after the splitting command , my compounds doesn’t appear in seperate folder. What should be done now ? Please help me

Thank you so much,.

Thanks so much for sharing this video. I have a question. I tried to use a command “obminimize” with my sdf files or mol2 files but it seemed to work with the first molecule only not every molecule that we want.

Hi there, great tutorial , I wanted to ask about how could'nt get the wildcard *.sdf to work in >obminimize -ff MMFF94 -n 1000 *.sdf and have to minimize my ligands one by one. Is it something particular to running obabel on Linux or could it down to the version of obabel you are using? Many Thanks Peter

Hello sir... I have written exactly the same script and am getting an error as Too many commandline parameters Can you please guide

hi i'm getting different results when i try to use the ADT manually. First I open ADT, then Ligand>open>file>save as pdbqt. When I try to do your method and compare the text files, the results are different.

it's very helpful thank u!

Sir, I have to include the spacing of gridbox also in config file, what I have to do?

i have drawn structures in chemdraw, i am not able to split them any suggestion? how to perform ?

thank you for your nicely elaborated video. I have one question. if in receptor molecule 3-4 chain present then what to do? And if there is inhibitor present with receptor molecule then how to remove?

Hi I want to do simultaneous multi-ligand coupling calculations in Autodock4. I have read articles on MLSD but still don't understand how to do it, it is confusing. Any advice? is there a protocol? Help please!!

Sir I followed the same steps for a ligand database i selected. I minimized those ligands using the script based method given but it didn't work. After that I started doing individually using Moe software using energy minimise option .But since i have more than 500 ligands it's a tedious job to do it individually.Pls help me because using the script my ligands didn't get minimized and also some of the double bonds got lost, some valencies also went wrong..

Sir, please make a video on redocking of cocrystallized ligand and rmsd calculation of it ( validation of docking by Redocking)

Good day sir. You are making great videos that are very helpful. Just got on question sir, really hope you can answer it. I have done docking and also experiment in the lab. let say I have 3 compounds name A, B and C as inhibitor to enzyme. In the docking A show better binding energy compared to B and C. However, experimentally B showed better result than A and C. B is more potent. What could be the reason that I got different result sir? Does it because I might perform docking wrongly?

Pls which field used for ammarge betwen ligand-receptor it IS mmf94?

my ligand file is not splitting by using the command. it says the file cannot be read. what is the issue?

Hi Sir, I downloaded sdf files from ChMBL and not able to split them into several files. Do you provide any specific tutorial on payment basis. I want to learn virtual screening for my PhD (such as using Zinc database). Kindly provide your detail so that I can contact you.

output name must be defined when docking simultaneously multiple ligands Kindly help

Good tutorial. May I ask how to to docking for aptamers and receptor using AutoDock Vina? Is it the same steps?

I still don't understand why you modelled the structure when its crystal structure was available.

Sir, thank you for very informative videos. How can we make the perl script file Sir. Please do guide.

While separating the ligand file, I get this error: "Open Babel Error in TetStereoToWedgeHash Failed to set stereochemistry as unable to find an available bond". I could not find how to solve it? Could you help me please?

Thank you for the video and it's very helpful. Can you show me/us how to dock ligands that have more than 32 rotational bonds and how to make a part of the ligands non-rotatable?

aotodock vina dont generates dlg files for acids?

perl command is not working in ubuntu.Please suggest

kindly ask how to get vina_linux file

Hello sir, I am facing problem in finding CharmM forcefield of molecules using Discovery Studio visualizer, can u please make a video on it please.

Sir... Your linux pl file is not opening...any other way to download it?

Sir, kindly show how to get the top 10 hits after virtual screening

Sir are you using a command prompt for splitting? because am facing problem during splitting of 100 substances

if its 430000 subcultures are there how to download it in sdf.

Very nice

Isn't it necessary to add gasteiger charges?

Thank you for the helpful video :) Is there any command to rank the output log files in order of their binding energy ?

Sir your video is very informative and has helped me a lot. I have a doubt regarding the perl script, in command line when I type perl Vina_windows.pl it shows no such directory is found. Can you guide me on this?

Sir, when converting to pdbqt, foes obabel automatically add gasteiger charges to ligands?

sir what is 2DAD IN CMD LINE YOU TYPING

This tutorial is great and very useful but "obminimize -ff (forcefield) -n (steps) *.sdf" command results in "cannot read input file"

Sir, I have a doubt. If structure for a protein is not given and we want to use it through homology modelling then how do we set grid size or we should go for blind docking ( I don't know about this) ?

thankyou sir for the such a informative video.. I could not download the zinc substances in .sdf format or if I download in .sdf.gz using wget method I could not extract the file

Hello I want to ask about Vina, I have put my ligand pdbqt and receptor pdbqt in the same folder. When I open Vina, it says missing receptor and keep closing. What should I do?

My ligands have been converted but there are no files generated. The ligands were converted but all are still in one file.... :( Btw im using linux

very helpful video sir 🙏 how can i find the perl script file pls share with us

Sir , How can we dock ligand with protein containing metal ions in their active site ...In autodock vina ?...( To find interaction of ligand with metallozymes)

Sir, say there are 20000 compounds to be screened, then how can I make the screening faster ? It is taking 11 hours for 20 ligands.

where can i find a python script for all of this?

Can someone please tell me how to download it on macOS?

i am actually using it on Ubuntu, i am getting errors : too many positional options have been specified on command line

Hello Sir I am Shikha Mudgal PhD scholar at AIIMS Rishikesh. We are doing some experiments on docking, sir will you please review our paper?

Sir, when executing command I get error. command line parse error: too many options. But i got the log files and output. Is it fine and how to resolve this error.

Please I couldnt know my sudo password

Thanks for preparing this easily understandable video tutorial. I have learned and replicated in my research. May I have your email address.