AutoDock 4 for Beginners | Molecular Docking Tutorial | Publication to Installation

This tutorial will introduce you to docking using the AutoDock suite of programs. We will use a Graphical User Interface called AutoDockTools, or ADT, that helps a user easily set up the two
molecules for docking, launches the external number crunching jobs in AutoDock, and when the dockings are completed also lets the user interactively visualize the docking results in 3D.
Sections:
0:00-2:00 Requirements
2:01-8:45 Theory
8:46-10:40 Installation of MGLTools
10:44-19:37 Protein and Ligand download and cleanup
19:38-28:20 Protein preparation using MGLTools
28:25-34:42 Ligand preparation using MGLTools
34:43-40:23 Grid box settings
40:25- 51:03 Running Autogrid4
51:05-59:25 Docking parameters
59:29-1:08:25 Running AutoDock4
1:08:26-1:29:30 Analyze conformations
1:29:32-1:43:38 Create publication quality figures using ChimeraX
1:34:38-1:37:43 Using Discovery studio for 2D interaction plot
1:40:00-1:43-34 Evaluation and comparison with experimental PDB structure
1:43:39-1:49:39 Inhibition constant Ki
AutoDock 4.2.6: autodock.scripps.edu/download...
MGL tools: ccsb.scripps.edu/mgltools/dow... (v.1.5.7)
MGLTools 1.5.6 documentation: ccsb.scripps.edu/mgltools/1-5-6/
Music
Almost in F - Tranquillity by Kevin MacLeod is licensed under a Creative Commons Attribution 4.0 license. creativecommons.org/licenses/...
Source: incompetech.com/music/royalty-...
Artist: incompetech.com/
#bioinformatics #tutorials #computational biology #molecular informatics #biophysics #molecular docking #beginners tutorial #how to do docking #molecular docking for beginners #UCSF chimera X #Discovery Studio Visualizer #Publication quality images #Using AutoDock 4 with
AutoDockTools:
A Tutorial #AutoDock 4 Tutorial | Installation to Publication #Using autodock tools for docking

[@cowboycatranch]

Only at one-third of this video, but so far you're an amazing teacher! Thank you so much. I hope you are available if any questions will arise later. Thank you again. General advice for anyone watching this tutorial: never use file names or folders with a space.

[@BioinfoCopilot]

Thank you very much for your suggestions. Much appreciated. I will try to solve any queries that arise. And hopefully I will make another video related to grid map settings to clear up all the doubts. 🙏

[@Olcool]

The best explained video on docking ever on KZbin. Well presented. Thanks alot. I am currently doing docking and this video become the life saver after struggling for long.

[@BioinfoCopilot]

Thank you very much @olcool ! Glad it was helpful!

[@kiyimbakennedy27793]

Wow. well explained. Thanks Very much for the video. you are a lifesaver. God bless

[@BioinfoCopilot]

My pleasure and thank you very much for your kind comment!

[@piergiorgiocianciullo6784]

Nice and clean ✌🏻👌🏻

[@theodiacouple6539]

Thanks

[@kyo_the13thzodiac]

Hi! Is there a way for me to automate docking multiple ligands for autodock4 instead of autodock vina? I have already docked my (356) ligands to autodock vina and I want to do the same for autodock4 so I can add their binding affinities for my thesis. Your response would be of great help. Thanks in advanced!

[@BioinfoCopilot]

You have to use Autodock4 GPU. Here is my GitHub repo and explanation how to use it. github.com/pritampanda15/AutodockGPU

[@preethanujpreethalayam4840]

Thank you very much for your nice videos and explanation! ... In setting The map type, I selected directly as you mentioned, and it appears like this [A C HD N NA OA SA] without F .. I tried to parameterize the fluorine atom. but I can't do that. Can you explain how to do that in more detailed way as you did in this video?

[@BioinfoCopilot]

Glad it helped! As I mentioned earlier, the parameterization of specific atoms or ion or metal types will be covered in another video if I reach 10k subscribers. I will definitely make a video about metal ions and other atoms docking. Thank you 🙏

[@alfredakinlalu8230]

Thanks for this well-presented tutorial. I tried using the "show interactions" option from the Analyze tab. But I keep getting a python error message, which in the accompany terminal is written as "swig/python detected a memory leak of type 'BHtree *', no destructor found." Do you have an idea the reason for this and how it may be resolved? I have tried searching on Google, but found nothing useful yet. Thanks

[@BioinfoCopilot]

Thank you very much. Please check this thread www.researchgate.net/post/Swig_python_BHtree_memory_leak_in_autodock_4_how_can_I_solve_it

[@salmafares3113]

Thank you for your helpful video but I have a problem, when pressing for autodock an error message shows up saying “ I cant find or open protein.C1 map “ any help please ???

[@BioinfoCopilot]

If you are using windows, then remember to put all your files in C drive. Then you can access all the files. Its tricky but watch my other videos on MGL tools.

[@rohillarajat]

Love from India ❤ lots of tnx🙏

[@BioinfoCopilot]

Thank you 🙏

[@rohillarajat]

@@BioinfoCopilot respected sir, I am a window user kindly tell me how i add upper tool like in your mac i see home button there all colure action is see i want to soft my image but i not found to soft image option any where like lighting option in home section

[@BioinfoCopilot]

@rohillarajat Probably you have to use Adobe illustrator or something similar to get more lighting or color options. In powerpoint also you can make good quality figures. But I would recommend to first convert to PDF and then convert to PNG image for better resolution

[@rohillarajat]

@@BioinfoCopilot tnxs sir🙏

[@user-er8mv8uy4y]

Thank you very much for your helpful videos! ... In setting The map type, I selected directly as you mentioned, and it appears like this [A C HD N NA OA SA] without F ... How can I solve this issue? .. Thanks again.

[@BioinfoCopilot]

You have to parameterise the atom name which is Fluorine in your case. You can find the parameters in AD4_Parameters.dat file

[@user-er8mv8uy4y]

@@BioinfoCopilot Thank you once again if you could elaborate more on this point.

[@gabrielbiancosilva5621]

Good morning, i have a doubt, do you know how the AutoDock make the Clustering process???? Which critery he uses so as to find and agroup similary poses??? Thanks for the attention.

[@BioinfoCopilot]

Yes the autodock makes clustering process by using RMSD as reference in which rms mode is unique pair. It performs ranked cluster analyses

[@johnmullins2491]

When I open 1.5.7 MGLTools, each app says it needs to be updated and contact developer. I tried using other versions but they won't work. Any advice? I have MacOS Ventura by the way

[@BioinfoCopilot]

MGL tools only works with previous version (before catalina). So I would recommend to install Parallels or any virtual OS. MGL tools latest version only works with windows and Linux.

[@wulikhang4610]

Thanks a lot for the explanation! Do you have any idea why the "preserve input receptor charges" dialog at 35:27 is not showing up on my computer?

[@wulikhang4610]

For those facing the same issue: you can restart autodocktools and drag the ligand and protein inside instead of importing them

[@juhidutta6121]

Still I have not got that dialog box.

[@diegosantiago9817]

This helped me out, thank you so much!

[@AltavistaVrn]

Thank you so much for your videos! You helped me a lot. Could you tell me please if I should click something in ADTools when the article says "each atom was assigned an “autodock type”? I tried to dock my ligand as it was showed by colleagues, but it posed "upside down".

[@BioinfoCopilot]

Thank you very much 🙏🏼. Check 26:00 to 27:00 where I have shown how to assign AD4 type. Also regarding the poses, check other poses as well. Increase the no. of poses in the dock.dpf to 50 and observe the difference! Thanks

[@cowboycatranch]

I saved the cluster file (write, save as .ps). I'm unable to open the .ps file and show the graph again. Could you please assist?

[@BioinfoCopilot]

.ps files can be opened using photoshop apps like Adobe. So, may be you save it using pdf or png format.

[@marcodegennaro4771]

Thanks for your videos! I have only one question: How can I get better graphics quality for autodock?

[@BioinfoCopilot]

Use autodock results and visualize using ChimeraX and 2D plot using DS visualizer. I have made a video related to how to generate publication quality figures. Check my videos.

[@marcodegennaro4771]

@@BioinfoCopilot Yes, I've seen it. But, my AutodockTools graphics it's very bad compared to yours!

[@BioinfoCopilot]

@@marcodegennaro4771 Have you installed the latest version. Anyway you can use chimeraX. Check out these videos: How to make publication quality figures | Part I | ChimeraX | Molecular Modeling & Drug Designing kzbin.info/www/bejne/n2nJZpiCpcebY8k and How to make publication-quality figures | Part 2 | Discovery Studio Visualizer | ChimeraX | Origin kzbin.info/www/bejne/jprGfZmKhbh0bdE

[@user-dv6uw5nl5g]

of all the docking tutorials, I found this is very amazing and you help me a lot. Three questions. 1. while preparing the protein, should the missing atoms be not repaired? there is option for that in the edit-Misc-check for missing atoms and then repair 2. while trying to set map types for the ligand, F did not appeard by default and even when i tried to set docking parameters for the ligand, can i add it manually? 3. like the ligand's geometry is optimized, should't the protein be optimized as well? because the protein usually is found bounded with ligands or any molecules in the pdb and when this ligands or molecules are removed there might be a need to optimize the energy caused by the bounded ligands. Thank you

[@BioinfoCopilot]

Thank you very much! 1. Missing atoms should be repaired using another program called SwissPDB Viewer. Unfortunately, there are no options to repair missing atoms. 2. You can add it manually but before that you need to know the parameters. You might have to quantum mechanical calcutions to achieve that. 3. For docking no. But after docking you can subject it for MD simulation. 4. You can achieve all the properties during MD simulation. Remember docking is a static process and MD is dynamic.

[@khadijaazzaoui5797]

Amazing tutorial ; but I have really a problem wich I can't get the glg fil ! What can I do to solve this problem? 🙏

[@BioinfoCopilot]

If you are using windows then I think the file gets locked at C drive. What you have to do is set the directory of your working folder first and then run.

[@chinnabandaru5103]

The entire session was very helpful 🎉🎉 explanation also very good sir I also did auto dock as same but i have doubt and problem after completion of docking how to get the delta G values and tables Where we will get the things please explain sir

[@BioinfoCopilot]

Thank you very much. Yes you can obtain these values from the dlg file that have been generated.

[@pradeepapradeepa3918]

Hi,after creating dlg file it shows unsuccessful, because it shows ligand pdpqt is missing ,,but ligand pdpqt is in destination folder,,what could be a reason,please say

[@BioinfoCopilot]

If it is in C drive then you have to give permission. Somehow in windows its hidden. Set the working directory in MGLtools. Go to file and set working directory.

[@cowboycatranch]

Is there a difference between "add all hydrogens" followed by "merge non-polar" versus "add polar hydrogens only"?

[@BioinfoCopilot]

There’s no difference but to maintain the receptor overall balance or so to say optimized one we do both the steps.

[@rohantembare2511]

Hi i have problem when run the docking it says : autogrid4: ERROR: Unknown receptor type: "Se" -- Add parameters for it to the parameter library first! How can I solve!

[@BioinfoCopilot]

You have to add atom parameters in AD4_prameters file and then run Autogrid4.

[@Olcool]

Greetings. Do you have a solution on the issue of docking large ligands with torsions more than 32? How can i solve this problem in Autodock 4?

[@BioinfoCopilot]

Thanks. Try DINC: a new AutoDock-based protocol for docking large ligands.

[@BioinfoCopilot]

Or else you can choose the ligand as flexible ligand and then set the number of torsion.

[@Olcool]

@@BioinfoCopilot Is the protocol the same? May you make a video tutorial on how to use it please if possible. I will be greatful.

[@BioinfoCopilot]

@olcool Sure I will try to. Thanks

[@sandhyajayakumar2692]

while adjusting grid parameters, even after maximizing the values also, my protein is not fitting into the grid box. help me to fix the issue sir

[@BioinfoCopilot]

Then switch to targeted docking. You can choose the active site using CastP and then do docking.

[@PrinceKumar-ct6cy]

I had the active site for my protein but when I docked by taking the mean x, y, z cordinated of all the known residue known for forming the active pocket, with the actual substrate of the protein (enzyme) it didn't had even the single same amino acid residue which makes the active pocket..... so please suggest me how to tackle this issue and where is the problem.... so I could proceed with docking the inhibitors... thanks

[@BioinfoCopilot]

First take a blind docking approach. Generate atleast 200 configurations. If you are satisfied then proceed. Else then take targeted docking approach and generate the same 200 configurations. Improve the algorithm by tweaking the autodock parameters while setting the docking parameters. One more thing, you select the exact residues from the known active site and then do targeted docking. Don’t take the mean.

[@PrinceKumar-ct6cy]

@@BioinfoCopilot First of all thank you for the response, and how to take the exact X, Y, Z coordinates because the active pocket consists of 5 amino acids each having different X, Y, Z coordinates..

[@BioinfoCopilot]

@@PrinceKumar-ct6cy You don’t have to take coordinates rather you select the residues in MGL tools GUI and then adjust the grid.

[@amirbuniatzade9919]

Hello amazing tutorial, I was just wondering if you know why autogrid won't do anything- like I don't even get the unsuccessful log file either, seems like nothing is happening when I run AutoGrid

[@BioinfoCopilot]

Thank you 🙏. Yes Autogrid does extensive operation in creating the grid and understanding the configuration of the system. When you open glg file after Autogrid, you can see all the descriptions.

[@priyajaiswal9299]

from where to open glg file

[@priyajaiswal9299]

i don't get any file after running autogrid

[@BioinfoCopilot]

@priyajaiswal9299 From your analysis folder. After running grid.gpf you might have got grid.glg. If you are running it on windows then the file must have been hidden. So its better to set the analysis directory first and then run analysis.

[@priyajaiswal9299]

where is the analysis directory

[@khanubaidurrahman8094]

I am trying protein 2QMJ with acarbose but Docking results are not generating But for others protein the results are generated. How to dock 2QMJ with acarbose please help.

[@BioinfoCopilot]

Well this is individual cases. So try to follow the instructions. If you have generated for others I am sure that you can

[@iqrahamid5240]

How to dock a complex ligand containing metal like Sn?

[@BioinfoCopilot]

Yes its is possible to dock chemical compounds containing metal ions. But I will make a video about it once I reach 10K subscribers. Thanks . Please subscribe and share.

[@y.anushyareddy3350]

Hi, ur video was very helpful for me, I just have a doubt about ligand, is it possible to dock heavy metals with proteins, and how to add new atoms to the auto dock file as it showing error: unknown atom....

[@BioinfoCopilot]

Yes that’s the tricky part. Adding meta ions is something you have to parameterize using Quantum physics based DFT methods.

[@y.anushyareddy3350]

@@BioinfoCopilot thanks for replying. While running autodock I'm able to get glg file for the added new parameters but it's not working for dlg( I think I'm missing some step), so, sir can u tell how to add the edited parameter file to dpf

[@BioinfoCopilot]

@@y.anushyareddy3350 The way you did for getting glg will also work for dpf file as well.

[@cowboycatranch]

In UCSF Chimera, the option "action > view" no longer exists. Can you please let us know what to do in Chimera version 1.7?

[@BioinfoCopilot]

You have to use UCSF Chimera X. Not the normal UCSF Chimera.

[@cowboycatranch]

I am using UCSF Chimera X. Happy to share a screenshot with you if you wish.@@BioinfoCopilot

[@cowboycatranch]

No response?

[@BioinfoCopilot]

@@cowboycatranch Read the documentation. Its easy to figure out.

[@gabrielbiancosilva7254]

Hello, good morning, i would like to know, what is a Cluster, What is population What is Cluster analyses, What is the diference between Lamarckian Genetic Algoritm and Genetic Algoritm, and I Also would like to know, if I Uncrease the number of population and Run, what that influences in the result???? Thanks for the attention. I'm a student from UFRJ, Brazil, I Work with molecular docking, i am really enjoying the research.

[@BioinfoCopilot]

Yes, you can play around with the parameters as you wish. It depends what conformations you are looking for? Is it relevant with the experimental data? AutoDock provides several methods for doing the conformation search. Currently, the Lamarckian Genetic Algorithm provides the most efficient search for general applications, and in most cases will be the technique used. It is typically effective for systems with about 10 rotatable bonds in the ligand. The Genetic Algorithm may also be run without the local search, but this is typically less efficient than the Lamarckian GA-LS combination. Simulated Annealing is also less efficient that the Lamarckian Genetic Algorithm, but it can be useful in applications where search starting from a given point is desired. Local Search may be used to optimize a molecule in its local environment.

[@houssemzitoun110]

hello , i am having a problem , when pressing show 2D diagram an error message shows up saying 'Ligand is not a single fragment'. Any help pls?

[@BioinfoCopilot]

You have to optimize the ligand. If you have metal ions in your ligand, then it might be problematic.

[@houssemzitoun110]

@@BioinfoCopilot and how can i do that?

[@BioinfoCopilot]

@@houssemzitoun110 Optimize the ligand again. While converting the ligand from sdf to pdbqt it might be broken. Check again and then dock the ligand. Do the conversion using chimera or open babel. Manually inspect the ligand before docking.

[@houssemzitoun110]

@@BioinfoCopilot thank you for your answer , but i fixed the problem, i have imported the pdb format not the pdbqt of the best ligand conformation and it worked. But , is it a problem that i see unfavorable acceptor acceptor in the 2D diagram?

[@priyajaiswal9299]

how to solve this error,.. too few value read in. Check grid map 'a'

[@BioinfoCopilot]

Please provide more details.

[@busemericacar36]

Thank you for your video, Is biovia discovery studio free or demo? If this program costly, could you say alternative program?

[@BioinfoCopilot]

DS Visualizer is free. Maestro is free. You can try both.

[@busemericacar36]

@@BioinfoCopilot thank you very much

[@abhishektripathi4533]

When I am trying to load .mol2 file of ligand. It is giving an attribute error. """""""AttributeError: 'str' object has no attribute 'allAtoms'""""""" It is quite confusing....I tried it many times.

[@BioinfoCopilot]

Because your ligand is not properly formatted. Use Avogadro to save the mol2 (sybyl) format and then upload it.

[@abhishektripathi4533]

@@BioinfoCopilot Okay! I will try.

[@juhidutta6121]

Hi, gromacs shows the protein charge is 3, but when Kollman charges were added, it shows 21 Kollman charges were added. Why is this discrepancy?

[@BioinfoCopilot]

Have you ignored the hydrogens using -ignh command in pdb2gmx command?

[@juhidutta6121]

@@BioinfoCopilot I have used the same command you used. Didn't use -ignh

[@busesahin5519]

wanna ask something.. The reference rmsd and cluster rmsd, what are they exactly and which menas what? how do i interpret the results?

[@busesahin5519]

isnt the reference rmsd values should be less than 2 angsgtrom?

[@BioinfoCopilot]

Cluster RMS is the root mean square difference in coordinates between this conformation and the cluster reference. Reference RMS is the rms difference between this structure and the input structure.

[@BioinfoCopilot]

If you have a reference ligand structure docked already (x-ray) then the position of the docked compound should be less than 2 Ang for best possible conformation

[@pradeepapradeepa3918]

While using macromolecules for protein for pdbqt it is coming as no non-bonded atoms is popping up in autodock tools ,,may I know the reason

[@BioinfoCopilot]

Use swiss pdb viewer to optimize the protein and also check for missing residues.

[@virendraracharla888]

@@BioinfoCopilot at 35 mins in the video while opening from grid-->macromolecules-->choose-->protein: am too getting-warning saying initializing protein.pdb:-contains no non-bonded atoms, shld i follow the same as mentioned above, ie using swiss pdb viewer for optimizing the protein and checking the missing residues----please ellaborate it I dont understand

[@BioinfoCopilot]

@virendraracharla888 Yes 👍

[@juanfernandosambranonarvae1656]

Por que usar optimización de estructura y no reducción de energía?

[@BioinfoCopilot]

Structure minimization is necessary to reduce the overall potential energy of the protein (receptor) and the ligand.

[@chinnabandaru5103]

Sir Which software we need for QSAR and ic50 values

[@ketaminehcl1248]

I use knime for it, you can use any provided workflow

[@chinnabandaru5103]

for QSAR STUDIES WE NEED ANY BIOLOGICAL ACTIVATION?@@ketaminehcl1248

[@BioinfoCopilot]

QSAR toolbox

[@drjagadishdasari2294]

Hi sir, Whenever I upload the Molecule in AUTODOCK this type of message comes "swig/python detected a memory leak of type 'BHtree *', no destructor found" and I am unable to see the Protein molecule ... I tried a lot of times by installing and uninstalling Can you please tell me a solution I am trying from so many days still the problem persisting ...........I am waiting for your reply ............Thanking you sir

[@BioinfoCopilot]

Uninstall and install again. Update the python version as well. If not solved, then check whether the protein has missing residues or not. If yes, then repair them using Swiss PDB Viewer.

[@user-wj1vv8kw2b]

Hello! does anyone have an idea on how to dock a ligand that can not be downloaded from the internet. Let's say for instance, I made new compounds in the lab and I aim to dock them in the active site of a receptor I have downloaded from PDB, how do I do this? does this tool have any chemdraw feature that allows restructuring of ligands? I hope someone responds, this is very vital to my work, I'd really appreciate. Thanks.

[@BioinfoCopilot]

Easy! Draw your chemical structure in chemdraw or chemsketch then save it as .sdf format. Open Avogadro, then optimize it and convert sdf to mol2. Then refer to my video and you can dock your ligands to the protein that you have downloaded. Follow my other videos as well how to convert sdf to pdbqt.

[@user-wj1vv8kw2b]

Awesome, thank you very much for the prompt response. @@BioinfoCopilot

[@user-wj1vv8kw2b]

You are amazing indeed! Thank you so much for your help, it worked. I am a bit concerned though, i tried doing a 100 runs but it is taking too long, is there a shorter way? or what is the major difference between running 10 vs 100 because i have a lot of compounds to run.

[@user-wj1vv8kw2b]

Hello, I have an issue, after drawing my ligand with chemdraw and saving in sdf format then using avogadro to save in mol2 format, i have gone further to dock but at the end, the structure of my ligand changes by some bond rearrangement. how do i correct this please?

[@user-wj1vv8kw2b]

Hi Nerdalytics, please i'd really appreciate if you can be so kind to answer my questions. I seem to be stucked. Thanks a bunch for your help so far.

[@emanhassan1851]

thanks alot for this helpful video. l run all steps in sequance , but docking not succesfully complete ... Fatal error , I can't find or open "protein C1. map" How can i solve this problem ?

[@emanhassan1851]

and some time the same problem but with different type of map file .. i.e, fatal error , I cannot find or open " F.map"

[@BioinfoCopilot]

Thank you! I think all your map files are in the C directory. I have mentioned how to change the directory and generate all the files. Carefully watch the video and try again. If the problem persists then contact me again.

[@emanhassan1851]

@@BioinfoCopilot thanks alot , I carefuly repeated all steps in sequance with different ligands ,docking was completed succefully with some ligands , but the same problem apeared again especially with ligand that contain F and Cl atoms

[@emanhassan1851]

Also, I want to ask about docking of ligands that containg metal ions like Cu , Ni , Co .. etc. How can i perform docking step by step?

[@BioinfoCopilot]

@@emanhassan1851 Metal docking is another concept which I will explain in my next video.

[@blankblank3709]

I encountred a problem in the "running autodock4" part, the doc.dlg file i get is not complete, and towards the end it is written : "I'm sorry; I can't find or open "Protein.F.map" ". How can i solve this sort of problems please ? thank you in advance.

[@BioinfoCopilot]

Check out the protein preparation step. If your protein contains metal ions, then it’s not going to generate the map. So remove any ions/metals from the protein and then prepare the protein for docking.

[@blankblank3709]

@@BioinfoCopilot I used the exact same protein and ligand you used in the tutorial, are there any extra steps i missed ?

[@BioinfoCopilot]

Then maybe do it again.

[@blankblank3709]

@@BioinfoCopilot I redid the entire process twice and i always get the same error in the same map generation step, is there any way i can remove the ions that are causing the problem ? Thank you.

[@BioinfoCopilot]

@blankblank3709 Refer to my other videos how to use Chimera. In Chimera you can remove ions and stuff and save it as protein.pdb. Also check whether you have file permissions or not in the working directory. If you are working on windows then check C drive file permissions as well.

[@ggiplum2350]

"Charges on carbons unchained" ERROR. How to solve this problem?

[@BioinfoCopilot]

This is topological error. You have to correctly define your protein or ligand. Preprocessing is necessary.

[@ketaminehcl1248]

when i run autogrid, the glg file is not created, how to fix it? please answer

[@BioinfoCopilot]

Check the log file (last couple of lines) and troubleshoot the error.

[@BioinfoCopilot]

Might be the problem with the file path or autogrid path. If you are using windows always look in the C drive

[@ketaminehcl1248]

@@BioinfoCopilot thanks

[@ERUMANSARI-q8v]

Hello sir I am beginners in docking please let me know what type of laptop configuration require for docking because i was following your method i did all things as you mentioned but when i go on autodock 4 in protein preparation it didn't show AD4 type. i m waiting for your reply

[@BioinfoCopilot]

A normal laptop with 8GB ram would work.

[@ERUMANSARI-q8v]

Thank you so. Much for your reply

[@ERUMANSARI-q8v]

I have already 8GB ram

[@BioinfoCopilot]

@ERUMANSARI-q8v Then no problem in performing docking.

[@amnaaftab84]

My files aren't converting into pdbqt files????

[@BioinfoCopilot]

Try once again and follow my tutorial

[@priyajaiswal9299]

i am unable to access glg file even though i changed the working directory

[@BioinfoCopilot]

Look in the C drive from where you executed Autodock or Autogrid

[@priyajaiswal9299]

nicely explained @@BioinfoCopilot

[@BioinfoCopilot]

Thanks 🙏

[@momogamer1433]

This video is probably the best in explaining how to use the autodock4 that I have seen so far!! I am quite confused. May I ask, when will we use Autodock4 and when will we use Autodock Vina? Thank you so much!

[@BioinfoCopilot]

Thank you very much! Autodock4 and Autodock vina serves equal purposes i.e. screening and docking. But the difference you might expect is that Autodock Vina is generally used to screen large number of compounds per se virtual screening whereas Autodock4 is mostly used for targeted docking where you exactly know the binding site. You can also use Autodock4 for simulated annealing and monte carlo.

[@momogamer1433]

@@BioinfoCopilot@BioinfoCopilot Currently, I'm trying to run a docking between polysaccharide and protein with 100 run/long as you suggested in the video, and it took 10 h. Is this normal, or should I change to using vina?

[@BioinfoCopilot]

@momogamer1433 Polysaccharides takes long time. So switch to vina and see how long it takes.

[@momogamer1433]

@@BioinfoCopilot Thank you so much:)

[@momogamer1433]

@@BioinfoCopilot If there is an influence of pH on both of the molecules that I am trying to dock, is it better to use GROMACs? P.S. I just finished the video, and got the data out! it looked amazing, I will definitely cite one of your papers :) I have also joined the membership. Thank you for having me as one of your students:)!

[@erenkasimfirtina7870]

There is a problem with my file saying that Grid data file needs the extension ".fld" for AVS input at run of grid.gpf file. Actually I made it whatever you did.

[@erenkasimfirtina7870]

Here is the problem code : C:/Program Files (x86)/The Scripps Research Institute/Autodock/4.2.6/autogrid4.exe: ERROR: Grid data file needs the extension ".fld" for AVS input

[@BioinfoCopilot]

@@erenkasimfirtina7870 Maybe try again generating the files (grid data).

[@erenkasimfirtina7870]

​@@BioinfoCopilot I had tried it a few times, but it didn't recover. Then it was determined that there was some space in the input file because of the name of the protein file. if you encounter a problem like this. Keep this in mind. Since we need to support each other, we can prove ourselves. By the way, your video is perfect.

[@BioinfoCopilot]

@erenkasimfirtina7870 Ohh I see. Yes I forgot to mention that any spaces or punctuations in naming the files e.g. receptor name for instance can lead to errors. This is a typical behavior of Python and thanks for pointing it out. Thank you very much! Much appreciated

[@jatinkashyap1491]

I want to use AutoDock GPU, which accepts protein.maps.fld and ligand.pdbqt files. Since I am performing high throughput virtual screening, shall I just load protein and follow the above tutorial to create protein.maps.fld file, which I can use in my command line run of AutoDock GPU run? I have 1 million ligands in my screening library, so can't repeat the above procedure on all ligands, or shall I just pick a ligand that contains all types of atoms a ligand can have in that ligand library and produce protein.maps.fld based upon that ligand along with the given protein?

[@BioinfoCopilot]

Yes, you can do it. I have used GPU version for 10000 ligands and it works. Here is the link: github.com/pritampanda15/AutodockGPU

[@ashirashid5950]

Hi, i am made lipid bilayer using charmm software and using it instead of protein. When i open the pdb of this lopid bilayer in autodock and try yo add hydrogen, i am getting error message saying the presence of nonbonded atoms. How can i fix it? Please guide

[@BioinfoCopilot]

You don’t need to do that. Lipid bilayer is different which you can’t add hydrogen using autodock. Autodock is for proteins. You have to perform all the steps in Charmm GUI only.

[@ashirashid5950]

@@BioinfoCopilot thank you for the guidance

[@RishabJain-un1vg]

It was really a good tutorial but I am facing an issue continuously that whenever I go on run autodock, set all the addresses and then launch.. the dialogue box appears and then immediately gets disappear without running ..earlier I was facing this problem while running autogrid but now thankfully from your tutorial..going step by step ..the auto grid worked but the same issue now is with running autodock even after keeping everything in a single destination folder.

[@BioinfoCopilot]

Check whether you have set the correct autodock parameters file on the dock.dpf. Then try again

[@RishabJain-un1vg]

​@@BioinfoCopilotyesss it is the right one..I checked many times

[@BioinfoCopilot]

Ok the what’s the error you are getting? Check the dlg file output at the end.

[@RishabJain-un1vg]

@@BioinfoCopilot the output says unsuccessful completion..while running the autodock option..the run box appears and the closes at the same time...just appears for one second on the screen..does not run

[@BioinfoCopilot]

@RishabJain-un1vg Write the full error message here. Not just unsuccessful completion but also the whole error message.

[@masroorkhalil9655]

ypur explanation method is like you are telling a story try to make it interesting

[@BioinfoCopilot]

Sure. Thanks

[@monikashringi1821]

C:/Users/devsh_sep0vuw/OneDrive/Desktop/research/4.2.6/autodock4.exe: FATAL ERROR: Sorry, I can't find or open AD4.1_bound.dat after run auto dock i m getting this error which shown in .dlg file how to solve this issue

[@BioinfoCopilot]

You have to run the application from C drive only not from Desktop. You can run from Desktop as well if you set the path in MGL tools

[@sheethaltresafernandes8217]

Great explanation Sir, I tried to follow every step in detail but in the end, I got this msg " FATAL ERROR: ERROR: 2963 records read in, but only dimensioned for 2048. Change "MAX_RECORDS" in "constants.h". How can I change the Max_ records? where will I find the constants.h? Please help. Your quick response is really commendable.

[@BioinfoCopilot]

Thank you. It might be your protein is too big and missing some residues or your ligand is too big. If you are running Autodock in windows then you cannot change the MAX RECORDS parameter. You can change the value in constants.h using linux and compile it. That can solve the error. Check your protein carefully. If it’s too big then it might cause a problem. Switch to Vina if it doesn’t work and follow the command line tutorial of vina.

[@sheethaltresafernandes8217]

Thanks a lot Sir. @@BioinfoCopilot