I want to thank you. Your video provided me with a quite clear and good understanding of the Autodock soft. Good job :) P.s. I also want to send " Hello" from young Belarusian biochemists to all people, who are engaged by modeling, docking, and science as well :)
I am a very beginner in this field of molecular docking. I have a query that the way we have Protein data bank, do we have compound data bank? Can we do docking on compounds as well?
Its really informative and very helpful. Great video but I would like to give one suggestion, don't get confused in the middle and don't rush. It's confusing the viewers as well.
Thank you so much. I could not use Mcule for an assignment b/c I needed to wait for a confirmation email that never came. This has a little bit more functionality but it has helped me greatly! Thanks!
I was following the tutorial until you jumped to the ligand selection. I wished you had specified where you got the ligand and showed us how you prepared the ligand (I know the preparation is the same as the target). Other than that, nice video!
if you got Error of all atoms don't have autodock element field while saving it in pdbqt format then after removing water--> adding H --> go to edit--> atom --> assign AD4 type then last step add Kolman charge and save it in pdbqt format.
Very informative. I have one query 47:11 ,the RMSD is more than 3 and as far i know i should be less than 2. so what is the reason for high RMSD and how can we reduce the RMSD?
Could you please explain about the ligand part too..how to select and prepare ligand ...its a humble request......and it will be so helpful in learning too...Thankyou.
This video is really helpfull...can you tell me to excute docking you have choosen option from "docking" instead of using "command prompt" and making a separate config file..so is the output results is same from both ways?
Please specify a receptor before trying to write a grid dimension file is popping up on screen when I clicked on output grid dimension file. How to do grid generation step to proceed ahead?
Very informative! One single problem, I have a Mac! and the installation process seems very different! Otherwise I guess the workflow will be the same right?
I am unable to download protein sequence file in pdb format... it is being downloaded in gaussian... Can u please suggest me what can I do to avoid it?
Does anyone know if there is a way to do docking if your ligand should be covalently attached to one of the amino acids with autodock vina? I have seen a lot of places directing to the same paper but even then I still can't figure it out...
good day, at first I thank you very much, I followed the steps but when I opend the ligand on autoduck it appears away from the macromolecule, not in it, so, how can I solve this problem.
I am facing this problem while docking after grid preparation. It is showing: C:/AutoDock/autodock4.exe: FATAL ERROR: ERROR: 2393 records read in, but only dimensioned for 2048. Change "MAX_RECORDS" in "constants.h". C:/AutoDock/autodock4.exe: Unsuccessful Completion. Please help, Sir.
Hello sir, I am docking for silver nanoclusters (instead of protein) with ligand but the Autogrid run is showing unsuccessful due to unknown receptor type. What should I do for that?
@Gate Chemistry Hello Sir! My protein is Penicillin Binding Protein 2a (pbp2a), I deleted the watermolecules, added polar hydrogens and kollman charges. I did'nt delete the Heteroatoms in the protein which are the natural ligands ( Cadmium and Chloride ions ). It does'nt have an inhibitor too. But still the protein is not getting saved in AutoDock. What might be the problem Sir? Is there anything to do with the valency? It's showing that all atoms do not have an autodock_element field. And also coming to the ligand, it's a cadmium ion and I downloaded the 2D SDF format from Pubchem. I tried converting it from sdf - - MDL MOL format to pdb format as pdbqt option is not there for this ligand in Openbabel. But even the saved ligand pdb file is not being displayed when I am trying to select the ligand for optimization. I am a beginner in Bioinformatics. Please help me with this if you could. Thank you!
I'm facing problem in the time grid... Not able to save the gile as pdbqt... After clicking grid, then select macro molecule, aftr selecting its show some problem...
I want to thank you. Your video provided me with a quite clear and good understanding of the Autodock soft. Good job :)
P.s. I also want to send " Hello" from young Belarusian biochemists to all people, who are engaged by modeling, docking, and science as well :)
Hey.
I am a very beginner in this field of molecular docking. I have a query that the way we have Protein data bank, do we have compound data bank? Can we do docking on compounds as well?
One of the best tutorials indeed.Thank you!
Its really informative and very helpful. Great video but I would like to give one suggestion, don't get confused in the middle and don't rush. It's confusing the viewers as well.
The best video on autodoc. A big thumbs up to you sir.
An excellent video. cleared all my doubts about Autodock. Excellent Presentation. Thank You
Thank you so much. I could not use Mcule for an assignment b/c I needed to wait for a confirmation email that never came. This has a little bit more functionality but it has helped me greatly! Thanks!
I was following the tutorial until you jumped to the ligand selection. I wished you had specified where you got the ligand and showed us how you prepared the ligand (I know the preparation is the same as the target). Other than that, nice video!
please tell how to download the ligand?
@@epicakku5381 From pubchem
Same problem 😢
Thank youuuu. It's because of your video that I realized why I'm having several failures in the docking. QAQ
Hi sir I followed your tutorial and got the results thank you so much for this session and please make more video like this 🙏
This video was of grt help .Thanku so much sir . Would like to learn more about this .
Wow, extremely on point i literally had a protein from covid aswell gj dude
Thank you so much. It provides a clear understanding on autodock software
It's really useful .
Best explanation .
Thank you soo much . Hope we will get more vedeos like this .
Thank you Sir, for providing the best tutorial on Auto doc
thank you so much sir, everything was so clear and perfect .thank you for making docking easier
Good explanation rather then other available video of autodock
I am using autodock 1.5.6
Waiting for more such video
sir plz use chimera software to remove C chain and prepare dock . It more easy
Great tutorial video, very helpful.... Keep making more videos on molecular docking
if you got Error of all atoms don't have autodock element field while saving it in pdbqt format then after removing water--> adding H --> go to edit--> atom --> assign AD4 type then last step add Kolman charge and save it in pdbqt format.
You saved my life!! Thank you so so much!!
Very detailed and precise explanation... Ty so much
As always explained in brief and clear .
Best tutorial on autodock...thank you sir
Excellent teaching. Thank you boss!!
Iam a research scholar (Biotech) really thank you❤❤....
Please help
What is the basic system requirements for the program run?
I'm a fresh student of don't have any idea about computer
This video is really good!! clear !!
Very informative. Thanks for the video
Exceptionally great 🎉🎉🎉
Thank you for your excellent video and explanation .it helped my assignment .on ligand where to download was not told still managed to complete
Thank you . Elaborated very well.
Very informative session........ thank you sir
Very helpful.
Thank you very much sir.
Very clearly explained... Thanks a lot😊
Amazing 👌. Helped me generate results.
Thank you so much for this .....plz make more videos
Good explanation. Thankyou
Thank you so much. That was indeed informative and something new to learn.
Thank a lot sir for making such an informative video.
Thanks for the content. Can you make a tutorial on protein - protein docking?
Thank you. Learnt something new.
Thanks. Nice tutorial.
Very well explained 👍
for getting ligand on the dock u done even need pymol u can just click on all molecule -- add molecule on the dock and aadd the file
Please help
What is the basic system requirements for the program run?
I'm a fresh student of don't have any idea about computer
Really good initiative
Thank you so much. It will be very useful
Very informative thank you for this session🤗
It is very helpful for me Bcz I am also same field like protein Ph. D 1st year student
I cant se how the ligand was downloaded.can you please help me with that?
very informative thank you very much
Very informative. I have one query 47:11 ,the RMSD is more than 3 and as far i know i should be less than 2. so what is the reason for high RMSD and how can we reduce the RMSD?
Thank you for this video
Great VDO. Request to make a video on Autodock VINA
Noted :)
@11:19 why did you add those 2 DAT files in the workspace?
Nice presentation.
Good initiative sir...thank u
Please make more videos on this topic..
If possible can you make tutorial video on Mestronova. Stay safe sir❤
Could you please explain about the ligand part too..how to select and prepare ligand ...its a humble request......and it will be so helpful in learning too...Thankyou.
A lot of respect🙏👍👍👍
Very Nice. One question, How to know which Ligand is best? If I have 5 ligands, each one docked?
thank you so much for your expalnation sir, i got the obstacle in add cofactor to reseptor, would you mind to help me for solve this problem?
Plz make videos of this series 🙏🏻
The best one thank you.
Pls make a video on pharmacophore mapping and md..Thanks once again
Sir you didn't mentioned which ligand you were using... Which made the tutorial useless for beginners like me. :'/
Exactly
why does it show all atoms do not have an autodock_element field
.pdbqt file is not generating when i try saving it as pdbqt?
do you need to add hydrogens for electron microscopy structures? Or just x-ray structures?
Thank you verry much. Can you help me please.
Why autodock vina does not generate the dlg files foor acids such as coumaric, caffeic, gallic ...etc?
Thank you so much!
what is the name of the ligand that you used?
best tutorial ever .i am facing error during grid generation .I am unable to get map data .where will be problem exist ?
Plz make video on MOT & d orbital splitting
Hello!
Many Thanks for such easy to use video on autodock...could please share a link for video on autodock vina.... if there is any
How should I convert affinity obtained into binding constant (kD)? At what temperature does Autodocvina runs?
Please make video on molden software for molecular designing
Excellent!
Sir, will you please make video on ligand ligand docking, is it possible?
This video is really helpfull...can you tell me to excute docking you have choosen option from "docking" instead of using "command prompt" and making a separate config file..so is the output results is same from both ways?
Thank you 🎉🎉
Please specify a receptor before trying to write a grid dimension file is popping up on screen when I clicked on output grid dimension file. How to do grid generation step to proceed ahead?
I have the same problem. Had you solved it? I would be very thankful for your help.
Sir I'm facing error after selecting grid>macromolecules>choose>select molecule and then error can you please help me 26:21
Very informative! One single problem, I have a Mac! and the installation process seems very different! Otherwise I guess the workflow will be the same right?
Can you explain please how to use the results for? For example if the ligand activates the protein or inhibit the protein?
Hi, can i ask you, which ligand is used in video?
Thx!
Thank you sir 👍
Can we save the receptor in pdbqt format just like the ligand? From save and write pdbqt
Hello sir it’s very informative video... i have a question that can we dock multiple ligands at one time with single protein with autodock4 ????
Thank you very much.
I am unable to download protein sequence file in pdb format... it is being downloaded in gaussian... Can u please suggest me what can I do to avoid it?
Nice and thanks
Excellent video. Can u provide this in pdf format
Does anyone know if there is a way to do docking if your ligand should be covalently attached to one of the amino acids with autodock vina? I have seen a lot of places directing to the same paper but even then I still can't figure it out...
good day, at first I thank you very much,
I followed the steps but when I opend the ligand on autoduck it appears away from the macromolecule, not in it, so, how can I solve this problem.
Hello sir why I get different docking score with autodock vina(with same protein and same ligand)?
Sir can you elaborate more about blind docking.?
Very helpful.. Can you please make a video on autodock vina? I have to use that but I'm getting an error in that
Do we need to Delete Water from Ligand??
I am facing this problem while docking after grid preparation. It is showing:
C:/AutoDock/autodock4.exe: FATAL ERROR: ERROR: 2393 records read in, but only dimensioned for 2048.
Change "MAX_RECORDS" in "constants.h".
C:/AutoDock/autodock4.exe: Unsuccessful Completion.
Please help, Sir.
Hello sir, I am docking for silver nanoclusters (instead of protein) with ligand but the Autogrid run is showing unsuccessful due to unknown receptor type. What should I do for that?
@Gate Chemistry Hello Sir! My protein is Penicillin Binding Protein 2a (pbp2a), I deleted the watermolecules, added polar hydrogens and kollman charges. I did'nt delete the Heteroatoms in the protein which are the natural ligands ( Cadmium and Chloride ions ). It does'nt have an inhibitor too. But still the protein is not getting saved in AutoDock. What might be the problem Sir? Is there anything to do with the valency? It's showing that all atoms do not have an autodock_element field. And also coming to the ligand, it's a cadmium ion and I downloaded the 2D SDF format from Pubchem. I tried converting it from sdf - - MDL MOL format to pdb format as pdbqt option is not there for this ligand in Openbabel. But even the saved ligand pdb file is not being displayed when I am trying to select the ligand for optimization. I am a beginner in Bioinformatics. Please help me with this if you could. Thank you!
Excellent..
I'm facing problem in the time grid... Not able to save the gile as pdbqt... After clicking grid, then select macro molecule, aftr selecting its show some problem...