Respected Madam Thank you so much, the video tutorial has helped a lot. I had one query, How can we visualise the interactions of amino acids with ligands? May you please help?
Excelent video, I want to ask how to know the best pose ? . You just have to count the number of H-Bound and check the distances ?. Another question, Do you know how to perform dynamic symulation with the docking results?
While doing docking is described in an article, it prepdocks the ligand, but in this video the minimized structure command is used. Which one would be right? Doing both, minimized structure or dock prep option?
Could you please tell me, how I can study metal, like Cdcl2 or PlCl2, I been trying to do the same approach but sadly it's not working? could anyone help me how to sort out?
mam I want to find out the interaction between the constructed synthetic gene with the cell surface marker protein, by which tool I can see the interaction
I t was nice but at the end its appearing as shown below.Kindly help me to sort out. Running AutoDock Vina for 3erd.pdb failed; see Reply Log for more information Application stderr ----- 'C:\Users\Dhanu\Desktop\molecular' is not recognized as an internal or external command, operable program or batch file.
Yes, you need to install autodock software only for this, as a result it will automatically create a folder in "Scrips research institute" named folder in your computer. But, if you are not using chimera for ligand and receptor preparation, then you may need to download some additional tools like MGL tools.
I think you (both) are asking for too much. In my opinion, it could be done with molecular dynamics, although I don't advise it since it's too much time consuming doing the animation for just a few femtoseconds (yes, you can only simulate that spending a long time haha)
I tried everything as it has been shown here! But my run also failed too. 1. Then I have found that the link for Autodock Vina shared here was only for windows 32 bit and mine is 64!! Anybody, can you help me to get AutoDock Vina for 64 bit? 2. Another thing I have noticed while looking at the protein and the ligand that there is a big gap between protein and ligand (al least 3 times more protein sized gap). Pulling up together did not work as well. suggestions??? Thanks In Advance.
Zeshan Haider hello Dr. I am a post graduate student from Nigeria and I have a project on docking. u tutorial has really been helpful but I can't download the chimera from UCSF website to practice it. I av tried it severally but the website doesn't load at all. is there a way u can help send a downloaded copy to my email. akekedeyemi@yahoo.com
perfect recommendation for beginners
I think it will be good if you also share a video about simulation..that can be very helpful for study of this interaction in detail.
Respected Madam
Thank you so much, the video tutorial has helped a lot.
I had one query, How can we visualise the interactions of amino acids with ligands? May you please help?
can not express how thishelpful .... well and very clear informative explanation (Y) great job , thanks alot
Mam, your video was very useful and it helped me for my project
Thank you mam, for uploading a very useful video. It was very easy to grasp you flow of work
Excellent presentation, very helpful!
Thanks for the video. Please, how do you adjust the grid box?
Excelent video, I want to ask how to know the best pose ? . You just have to count the number of H-Bound and check the distances ?. Another question, Do you know how to perform dynamic symulation with the docking results?
While doing docking is described in an article, it prepdocks the ligand, but in this video the minimized structure command is used. Which one would be right? Doing both, minimized structure or dock prep option?
Madam here showing receptor and ligand can not be the same model. Please can you suggest. Thank you madam
can anyone tell me how to install vina? the profesor said that I needed to copy the files in Vina folder to molecular docking directory. what is it?
Thank you for good presentation. can you help me for my docking study because no free online program are available /
There is no demnostration of the autodock vina installation or application. COuld you please make a video for this
Is it possible to do batch preparation using Chimera? We are using Marvin Sketch to generate the 3D conformers before loading in PyRx/Vina
The Autodock server is down. Couldn't download the autodock software. any help will be appreciated!!!
Thank you ,but in 44:34 idont have vina.exe what i do or where i get it?
Good morning, i interested to watch this video, miss can i ask about the chimera??🙏🙏
If I use isomeric SMILES rather than canonical SMILES of a molecule, can CHIMERA tell the difference between two enantiomers?
if you have some more video tutorial please provide me the link
ruclips.net/video/yBp74iHP9rA/видео.html
how to do structural comparison by using this software?
Could you please tell me, how I can study metal, like Cdcl2 or PlCl2, I been trying to do the same approach but sadly it's not working? could anyone help me how to sort out?
Hi, is this a docking with rigid protein and flexible ligand?
12:20 docking, challanges
This is extremely helpful, thank you!
wow that was really helpful! 😇 Thankyou
I think docking by autodock vina is more easy than in csf chimera
Can we do docking for multiple ligands with one protein molecule ?
nice presentation
it's very interesting, just a question, the translation, more explication please?!
very useful video, like it
very nyc and informative video, but can u please share docking with a receptor with the library of compounds using Autodock Vina.
Mala Sharma are u pharmacy student? How did u end up learning docking n how much u know?
Thanks for your help.
good work
mam I want to find out the interaction between the constructed synthetic gene with the cell surface marker protein, by which tool I can see the interaction
also interested to know more about that , if you've found something tell us :)
great but the auido was a little bad but no matter what it was amazing thanks a lot!
Presentation is nice, just the sound is bad
I t was nice but at the end its appearing as shown below.Kindly help me to sort out.
Running AutoDock Vina for 3erd.pdb failed; see Reply Log for more information
Application stderr
-----
'C:\Users\Dhanu\Desktop\molecular' is not recognized as an internal or external command,
operable program or batch file.
same here. Autodock running is failing again and again.
I don't know if you tried to follow the instructions autodock.scripps.edu/faqs-help/tutorial/using-autodock-4-with-autodocktools/2012_ADTtut.pdf
Anyways, it's easy to run autodock vina
I can help you if you need it, btw I'm linux user since the software runs better in linux than windows, but it's a pain in the ass to install it haha
In my case, my chimera, haven't auto doc vina? any suggestion.
You will have to download auto doc vina, i think then chimera will show it.
45:15 an error that says "too many heavy atoms (>100) in ligand" always appears just after I click ok. What should i do?
I've had this error before when I invert the selection of the ligand and the receptor.
Same!! My thesis is due in a couple of days and I'm unable to resolve this issue.
In video 44:17 how to get autodock vena.exe file.. whether I have to install autodock software?
Yes, you need to install autodock software only for this, as a result it will automatically create a folder in "Scrips research institute" named folder in your computer. But, if you are not using chimera for ligand and receptor preparation, then you may need to download some additional tools like MGL tools.
I am not able to get the results.
how we can observe the interaction of cell wall with proteins like endolysins of bacteriophage
i need software for the find out the interaction between biological molecules (protein, lipid and enzymes)and heavy metals (nickel nitrate)
I think you (both) are asking for too much. In my opinion, it could be done with molecular dynamics, although I don't advise it since it's too much time consuming doing the animation for just a few femtoseconds (yes, you can only simulate that spending a long time haha)
if anyone has step by step process written like a flowchart
How to download this software?
I tried everything as it has been shown here! But my run also failed too.
1. Then I have found that the link for Autodock Vina shared here was only for windows 32 bit and mine is 64!! Anybody, can you help me to get AutoDock Vina for 64 bit?
2. Another thing I have noticed while looking at the protein and the ligand that there is a big gap between protein and ligand (al least 3 times more protein sized gap). Pulling up together did not work as well. suggestions??? Thanks In Advance.
anyone can send me autodock vina scripts or how to donlod on window?
Zeshan Haider hello Dr. I am a post graduate student from Nigeria and I have a project on docking. u tutorial has really been helpful but I can't download the chimera from UCSF website to practice it. I av tried it severally but the website doesn't load at all. is there a way u can help send a downloaded copy to my email. akekedeyemi@yahoo.com
I prefer a windows copy cos I use windows
its perfect.
proteins.. i love the funky lookin little guys
very good Thank u :)