Please do keep making this type of videos it's very helpful
@jaannawaz20073 жыл бұрын
I will try my best
@souvikmitra43574 ай бұрын
The best video on KZbin... thank you very much sir
@danishiqbal77742 жыл бұрын
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.
@danishiqbal77742 жыл бұрын
I tried this command line but only blank file of results generated, there is no data present. I use windows laptop, kindly tell me what i am missing
@zeinabmohammadi35322 жыл бұрын
That is an excellent video. I'm really really thanks for it.be a successful and happy, dear doctor
@hamzadar90212 жыл бұрын
I still don't understand why you modelled the structure when its crystal structure was available.
@mercystephen85112 жыл бұрын
Thank you ❤️ for making this video it solved my doubts about docking multiple ligands.
@abhishektripathi4533 Жыл бұрын
I am getting the following error: "Command line parse error: unrecognised option '--log'" and "Output name must be defined when docking simultaneously multiple ligands." Kindly help.
@sanjaisrao4842 жыл бұрын
Thankyou very much , it was so useful
@efedogukandincel29593 жыл бұрын
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?
@gutterball102 жыл бұрын
@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.
@followermarket85972 жыл бұрын
Same problem with mine
@gutterball102 жыл бұрын
@Follower market, If you were able to make it this far, i suggest just executing the perl command in regular command prompt as shown in the last video, and then compiling the results file in ubuntu. I did this and it worked just fine.
@abhishektripathi4533 Жыл бұрын
I am getting the following error: "Command line parse error: unrecognised option '--log'" and "Output name must be defined when docking simultaneously multiple ligands." Kindly help.
@gutterball10 Жыл бұрын
@@abhishektripathi4533 I am no expert, however it is possible this software is not able to do mutlipe simultaneous ligand docking. I think it only docks 1 molecule at a time. Effectively this means that alosteric interactions and induced fit aspects of binding caused by multiple ligands binding simultaneously might not be accurately captured by the software.
@abhishektripathi4533 Жыл бұрын
@@gutterball10 You know after certain permutations, I found that you can perform the whole process in ubuntu as explained in this video, but only for the docking step, you can refer windows command prompt (just like the last video of virtual screening). After this, you go with ubuntu to get all the result files in a single file.
@srdjan81653 жыл бұрын
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?
@anshikagupta43013 жыл бұрын
Thanku so much again for this wonderful session.
@jaannawaz20073 жыл бұрын
Always welcome
@anshikagupta43012 жыл бұрын
Sir after using this script from more than one year ... i wanted to ask that can we increase no. Of cores in the script..
@srutishreesarma487026 күн бұрын
sir, can you tell which scoring is used in this method, AutoDock 4 or Vian scoring function?
@msaikirtikrishnan60562 жыл бұрын
Worked😄Thank you so much!!!
@smraza92 жыл бұрын
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
@manishagurnani92343 жыл бұрын
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.
@gutterball102 жыл бұрын
kolman charges are used to represent charged amino acids on the recptor and gastegier charges are used to represent charges on the ligand. The receptors and ligands need to have appropriate charges on them to represent what they would be in physiological conditions if you want the computation to model a result as close to real-life as possible.
@sphamandlamtambo46242 жыл бұрын
Thank you so much,.
@priyankhasridhar73482 жыл бұрын
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.
@Andy-iy7hd3 жыл бұрын
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!
@reemabutayeh3143 Жыл бұрын
Wer you able to find an answer? Iam interested
@CheerioChronicles11 ай бұрын
have you resolved your query, i want to know, how?
@Andy-iy7hd11 ай бұрын
No, I'm sorry, I never quite figured this one out .
@ManishKumar-cr4ue3 жыл бұрын
Sir how we can dock a rigid protein and multiple flexible proteins at once. Waiting for your reply.
@manojdhameja42123 жыл бұрын
Sir, please make a video on redocking of cocrystallized ligand and rmsd calculation of it ( validation of docking by Redocking)
@oktavialisti1723 жыл бұрын
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?
@blister9813 жыл бұрын
perl command is not working in ubuntu.Please suggest
@biswambharbiswas3590 Жыл бұрын
could you fix it? I'm also having same problem
@rumudas72996 ай бұрын
Hello sir , after the splitting command , my compounds doesn’t appear in seperate folder. What should be done now ? Please help me
@user-jy5hl5bz4y3 жыл бұрын
it's very helpful thank u!
@jaannawaz20073 жыл бұрын
Glad to hear that!
@njongkon41042 жыл бұрын
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.
@robertsonrivera97752 жыл бұрын
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.
@geekogenius Жыл бұрын
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
@petelok99692 жыл бұрын
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
@sagar1759 Жыл бұрын
i have drawn structures in chemdraw, i am not able to split them any suggestion? how to perform ?
@poojaprajapati9171 Жыл бұрын
Hello sir... I have written exactly the same script and am getting an error as Too many commandline parameters Can you please guide
@anjum3873 Жыл бұрын
Sir, I have to include the spacing of gridbox also in config file, what I have to do?
@vikalpsingh3367 Жыл бұрын
my ligand file is not splitting by using the command. it says the file cannot be read. what is the issue?
@nurfathini37703 жыл бұрын
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?
@jaannawaz20073 жыл бұрын
Autodock is not a great tool to perform docking if u have more than 15 rotatable bonds, if ur thinking about 32 rotatable bonds, its highly unlikely u will get good results from autodock. One thing u can do, You can reduce the rotatable bonds and run the docking. Once u perform the docking, you always have an option of molecular dynamics simulation
@nurfathini37703 жыл бұрын
@@jaannawaz2007 thank you, sir
@vinusujithamichael23143 жыл бұрын
Should we do this limiting the torsion to 15 for every ligand one by one ?
@ilgaztastekil66332 жыл бұрын
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?
@sumitmallick79513 жыл бұрын
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?
@jaannawaz20073 жыл бұрын
1. If u want to use receptor consist of 4 chains, it is possible in autodock, as Autodock considers a protein as rigid entity. 2. Check my previous video on Autodock
@RAVISINGH-hd8hf3 жыл бұрын
Very nice
@jaannawaz20073 жыл бұрын
Thanks
@nurlianafarhana72413 жыл бұрын
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?
@gutterball102 жыл бұрын
generally speaking, real life experimental results will be more valid than computational results. The computer results are only as good as the models and parameters used. There are always many confounding factors that need to be considered.
@carlosnaranjo76333 жыл бұрын
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!!
@salim48213 жыл бұрын
Pls which field used for ammarge betwen ligand-receptor it IS mmf94?
@bastiwala08083 жыл бұрын
kindly ask how to get vina_linux file
@bharathchandran87862 жыл бұрын
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..
@Doodlemelon3004 Жыл бұрын
output name must be defined when docking simultaneously multiple ligands Kindly help
@rupanyselvam80073 жыл бұрын
Good tutorial. May I ask how to to docking for aptamers and receptor using AutoDock Vina? Is it the same steps?
@gutterball102 жыл бұрын
autodock works best for screening of small molecule ligands to a target receptor, for larger molecules like peptides or aptamers, you might need to use different software. Not sure if professor BB provides other training videos on this topic, haven't watched through the rest of his library yet.
@kessaria923 жыл бұрын
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
@user-wy2ud3rx9j3 жыл бұрын
same problem with windows, have find a solution?
@kessaria923 жыл бұрын
@@user-wy2ud3rx9j no
@drsushreesangitamohapatra4017 Жыл бұрын
Sir, thank you for very informative videos. How can we make the perl script file Sir. Please do guide.
@e0n6622 жыл бұрын
Sir, when converting to pdbqt, foes obabel automatically add gasteiger charges to ligands?
@muzakabeer Жыл бұрын
gasteiger is default charge in openbabel
@vjharitalks10 ай бұрын
Isn't it necessary to add gasteiger charges?
@vjharitalks10 ай бұрын
Will converting SDF to pdbqt add up gasteiger charges?
@SEEMAUNNIKRISHNAN-mw9rt5 ай бұрын
if its 430000 subcultures are there how to download it in sdf.
@anjaliparcha6587 Жыл бұрын
Sir... Your linux pl file is not opening...any other way to download it?
@ramkumarkatturajan54743 жыл бұрын
This tutorial is great and very useful but "obminimize -ff (forcefield) -n (steps) *.sdf" command results in "cannot read input file"
@ramkumarkatturajan54743 жыл бұрын
Sir could you please help me to rectify this issue
@teuzen79003 жыл бұрын
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?
@jaannawaz20073 жыл бұрын
empty ur desktop and try again
@EM-bw7fs2 жыл бұрын
aotodock vina dont generates dlg files for acids?
@komaltilwani30293 жыл бұрын
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
@jaannawaz20073 жыл бұрын
try right click extract to folder...
@thoughts_of_indian_student3750 Жыл бұрын
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.
@dileepdn94643 жыл бұрын
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.
@ShakilurRahman3 жыл бұрын
Sir, kindly show how to get the top 10 hits after virtual screening
@thoughts_of_indian_student37503 жыл бұрын
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) ?
@jaannawaz20073 жыл бұрын
If active site amino acid known, u can setup spcific grid, if active site unknow u can use blind docking (create grid box for whole protein).
@thoughts_of_indian_student37503 жыл бұрын
@@jaannawaz2007 Could tell about how to analyze Vina results and go for simulation using gromacs. Your videos are very helpful. I am following your videos and I have learnt a lot. Please sir guide for future work on how to analyze vina results and then go for protein ligand simulation
@shreyasrivastava89953 жыл бұрын
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?
@gutterball102 жыл бұрын
Follow the steps from the previous tutorial on vina more carefully. 1) you need to make sure perl is installed on the computer. 2) you need to manually set-up the perl script file. He provides the code in the description in the previous vina tutorial video.
@squareroot2success3 жыл бұрын
Thank you for the helpful video :) Is there any command to rank the output log files in order of their binding energy ?
@jaannawaz20073 жыл бұрын
will update soon
@srdjan81653 жыл бұрын
Hello, did you get to know how to tank them?
@sounoksengupta87532 жыл бұрын
sir what is 2DAD IN CMD LINE YOU TYPING
@mastersourabh113 жыл бұрын
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)
@jaannawaz20073 жыл бұрын
hi... many metal ions are not included in the autodock forcefield, But, there is option available to add new atoms... check this link... autodock.scripps.edu/faqs-help/how-to/adding-new-atom-parameters-to-autodock
@mastersourabh113 жыл бұрын
@@jaannawaz2007 Ohkay.. Thank you sir. But how can get these parameters for our desired metal ion.. Are there any resources ?
@anaghabodkhe73289 ай бұрын
Can someone please tell me how to download it on macOS?
@jaidevsharma5702 жыл бұрын
i am actually using it on Ubuntu, i am getting errors : too many positional options have been specified on command line
@SoumyaduttaBasak9 ай бұрын
Hey I am getting the same error . How did you resolve it ?
@vinusujithamichael23143 жыл бұрын
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.
@jaannawaz20073 жыл бұрын
need to work on workstations or u need to increase the specs of ur computers
@gutterball102 жыл бұрын
use a more powerful computer.
@muzakabeer Жыл бұрын
you must have gpu a grpahics card which can be ascessed using CUDA
@user-wc8ys3uo2b Жыл бұрын
very helpful video sir 🙏 how can i find the perl script file pls share with us
@shikhamudgal94183 жыл бұрын
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?
@jaannawaz20073 жыл бұрын
Sure
@shikhamudgal94183 жыл бұрын
@@jaannawaz2007 Thank you. May I have your email id, to mail you the paper.
@abhishektripathi4533 Жыл бұрын
I am getting the following error: "Command line parse error: unrecognised option '--log'" and "Output name must be defined when docking simultaneously multiple ligands." Kindly help.
@siranodhe-paganon27192 жыл бұрын
where can i find a python script for all of this?
@thoughts_of_indian_student37503 жыл бұрын
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.
@manishagurnani92343 жыл бұрын
same error is with me sir kindly help us.
@hsd_masti18583 жыл бұрын
@@manishagurnani9234 I think there is no problem. You can check the output if it executed successfully.
@fozshub49153 жыл бұрын
Please I couldnt know my sudo password
@Viralworldremix2 жыл бұрын
Thanks for preparing this easily understandable video tutorial. I have learned and replicated in my research. May I have your email address.
@anumnaz66653 жыл бұрын
Sir are you using a command prompt for splitting? because am facing problem during splitting of 100 substances
@gutterball102 жыл бұрын
This process is being carried out through the ubuntu command line interface, not windows cmd interface.