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.
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 getting the following error: "Command line parse error: unrecognised option '--log'" and "Output name must be defined when docking simultaneously multiple ligands." Kindly help.
@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.
@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.
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.
@@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.
@@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.
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?
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.
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!
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.
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.
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 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?
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 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.
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!!
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
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..
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?
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.
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.
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?
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?
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
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.
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) ?
@@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
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?
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
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?
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.
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)
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
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
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.
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.
Please do keep making this type of videos it's very helpful
I will try my best
The best video on RUclips... thank you very much sir
I still don't understand why you modelled the structure when its crystal structure was available.
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.
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
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?
Thankyou very much , it was so useful
Thank you ❤️ for making this video it solved my doubts about docking multiple ligands.
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.
@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.
Same problem with mine
@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.
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.
@@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.
@@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.
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?
Hello sir , after the splitting command , my compounds doesn’t appear in seperate folder. What should be done now ? Please help me
sir, can you tell which scoring is used in this method, AutoDock 4 or Vian scoring function?
Sir how we can dock a rigid protein and multiple flexible proteins at once. Waiting for
your reply.
my ligand file is not splitting by using the command. it says the file cannot be read. what is the issue?
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.
Hello sir... I have written exactly the same script and am getting an error as
Too many commandline parameters
Can you please guide
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!
Wer you able to find an answer? Iam interested
have you resolved your query, i want to know, how?
No, I'm sorry, I never quite figured this one out
.
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.
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.
perl command is not working in ubuntu.Please suggest
could you fix it? I'm also having same problem
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?
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
Worked😄Thank you so much!!!
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?
Sir... Your linux pl file is not opening...any other way to download it?
kindly ask how to get vina_linux file
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.
i have drawn structures in chemdraw, i am not able to split them any suggestion? how to perform ?
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.
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!!
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
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..
output name must be defined when docking simultaneously multiple ligands
Kindly help
Thanku so much again for this wonderful session.
Always welcome
Sir after using this script from more than one year ... i wanted to ask that can we increase no. Of cores in the script..
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
Thank you so much,.
Sir, I have to include the spacing of gridbox also in config file, what I have to 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
same problem with windows, have find a solution?
@@user-wy2ud3rx9j no
if its 430000 subcultures are there how to download it in sdf.
Sir, please make a video on redocking of cocrystallized ligand and rmsd calculation of it ( validation of docking by Redocking)
aotodock vina dont generates dlg files for acids?
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?
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.
it's very helpful thank u!
Glad to hear that!
Pls which field used for ammarge betwen ligand-receptor it IS mmf94?
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.
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?
empty ur desktop and try again
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?
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
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.
Good tutorial. May I ask how to to docking for aptamers and receptor using AutoDock Vina? Is it the same steps?
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.
Isn't it necessary to add gasteiger charges?
Will converting SDF to pdbqt add up gasteiger charges?
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) ?
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).
@@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
Can someone please tell me how to download it on macOS?
Sir, thank you for very informative videos. How can we make the perl script file Sir. Please do guide.
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?
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
@@jaannawaz2007 thank you, sir
Should we do this limiting the torsion to 15 for every ligand one by one ?
i am actually using it on Ubuntu, i am getting errors : too many positional options have been specified on command line
Hey I am getting the same error . How did you resolve it ?
sir what is 2DAD IN CMD LINE YOU TYPING
where can i find a python script for all of this?
Sir, when converting to pdbqt, foes obabel automatically add gasteiger charges to ligands?
gasteiger is default charge in openbabel
Thank you for the helpful video :) Is there any command to rank the output log files in order of their binding energy ?
will update soon
Hello, did you get to know how to tank them?
Very nice
Thanks
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?
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.
Sir, kindly show how to get the top 10 hits after virtual screening
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)
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
@@jaannawaz2007 Ohkay.. Thank you sir. But how can get these parameters for our desired metal ion.. Are there any resources ?
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.
need to work on workstations or u need to increase the specs of ur computers
use a more powerful computer.
you must have gpu a grpahics card which can be ascessed using CUDA
This tutorial is great and very useful but "obminimize -ff (forcefield) -n (steps) *.sdf" command results in "cannot read input file"
Sir could you please help me to rectify this issue
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
try right click extract to folder...
very helpful video sir 🙏
how can i find the perl script file pls share with us
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.
same error is with me
sir kindly help us.
@@manishagurnani9234 I think there is no problem. You can check the output if it executed successfully.
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?
Sure
@@jaannawaz2007 Thank you. May I have your email id, to mail you the paper.
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.
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.
Sir are you using a command prompt for splitting? because am facing problem during splitting of 100 substances
This process is being carried out through the ubuntu command line interface, not windows cmd interface.