EP 1 | MOLECULAR DOCKING in UCSF CHIMERA by VINA Plugin from Scratch in Linux
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- Опубликовано: 30 авг 2022
- Hi,
I am Dr. Dweipayan Goswami,
Welcome to my RUclips channel "Learn at ease"
I will be uploading animated videos related to biochemistry for the Under Graduates and Graduates purely based on the information form the traditional text books
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Key links
UCSF CHIMERA : www.cgl.ucsf.edu/chimera/down...
AutoDock Vina Download : vina.scripps.edu/downloads/ 
Наука
Dr. Dweipayan Goswami! Thank you for this video! I couldn't find an error in my docking. After your video - I did it well! 1000 thanks and I wish you all the best!
The most detailed video on RUclips on this topic. Thanks a lot for your effort sir.
THANK YOU!!! This is so clearly explained.
Amazing explanation!!! thank you so much!!!
Thank you so much, it was amazing
veryyyy useful
Vai awesome
Does the resolution for the protein or receptor need to be low? If your answer is "yes", can I know why?
respected sir, plz make video on docking by autodock tool
Evrything went perfect until the (7:00)sudo command, it says it wasnt recognised as an internal or external command or batch file. How to fix that?
Sir, can you explain how to run hole2 programme for protein pore calculation
Hi Dr. Dweipayan Goswami,
While performing docking using VINA library in chimera, It throws an error saying "too many heavy atoms (>100) in ligand chimera docking". Does chimera offer VINA docking only for very small molecules (atoms < 100) or I am doing something wrong? How to get it done?
Thanks
There might be some error in steps performed..
The Pose1.pdb file is not prefixing the lines for the atoms of the ligand with "HETATM" They are all prefixed with ATOM. That might be why if I am just putting the poae1.pdb file into PyMol, it is only rendering the protein and is not "seeing" the ligand.... actaully I just had to select "All States" in Pymol
Can I perform it at windows ?
Hi
Good video, but I have a question. When you save the pose 1 you merge the naked_protein and the pose with the best affinity, but you have done the docking with the prepared_protein.mol2, so wouldn't be more correct to save the pose 1 with the protein_prepared and the ligand insted of the naked_protein? Because well, you performed the calculations with the prepared structure
Thanks and I hope I have explained to you correctly
Mol 2 files changes the numbers of amino acids of the protein which creates problem in understanding protein ligand interaction... Hence when u save the pose use the naked protein file which is in pdb format so all elements of files are not altered .
@@DweipayanG But, for example I've I saved the protein_prepared in pdb instead of mol2, the step in the MD simulation where I prepared the protein wouldn't be necessary, or I am wrong??
Please sir,
can you please do this mac os!
32.10 min. I am not able to creat mol2 file. I am following all the steps u mentioned ...still i am not able to creat....what could be the reason
There shouldn't be an issue .. i cannot say without seeing an error ... Just repeat the exact same steps with another ligand .... Or after minimizing ligand go to Files > Save .mol2
I have one question
Sir, I am getting an error "Too many heavy atoms (>100) in ligand"? I am Docking receptor as protein and hormone as ligand both files were taken from PDB in .pdb format is ok?
Ligand file has to be a .mol2 file
@@DweipayanG Sir, alreday did as per your guidelines but at the end i got the error.
@@DweipayanG i got two files protein.mol2 and ligand.mol2 both were run through chimera- autodockvina after "apply" key get error prompt
In the last step i guess u have chosen protein as ligand and ligand as receptor in the top part of vinna panel !
@@DweipayanG Sir, this is my second attempt to perform docking by watching your lecture series. last time was done successfully, this time I think both are kind of protein which cz the error.
How to do check the superimposed between original legad and and docked legand and it's impossible to to superimposed between Other
Its possible in ucsf chimera and i have shown that in my videos too how to do that …
@@DweipayanG
If that occur that means the docked ligand and co-crystalized ligand are same ??
@@DweipayanG
I see your co cryslazed ligand and docked ligand are same ?
Please explain sir
Hi Sir. Thanks for sharing this video. I have a problem. I am getting an Chimera Error: "Running AutoDock Vina for Protein_naked.pdb failed; see Reply Log for more information."
Details:
Model 0 (Protein_naked.pdb) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
energy cutoff -0.5
minimum helix length 3
minimum strand length 3
Use command 'help ksdssp' for more information.
No SEQRES records for Protein_naked.pdb (#0) chain A; guessing terminii instead
Chain-initial residues that are actual N terminii: #0 ASN 1.A
Chain-initial residues that are not actual N terminii:
Chain-final residues that are actual C terminii:
Chain-final residues that are not actual C terminii: #0 HIS 423.A
451 hydrogen bonds
Removing spurious proton from 'C' of #0 HIS 423.A
Hydrogens added
Wrote D:\Data\Desktop\6CM4\Risperidone\docking.receptor.pdb
adding gasteiger charges to peptide
Sorry, there are no Gasteiger parameters available for atom docking.receptor:A:GLN346:O
Wrote D:\Data\Desktop\6CM4\Risperidone\docking.ligand.pdb
Autodock Vina ligand docking initiated for Protein_naked.pdb
Traceback (most recent call last):
File "C:\Program Files\Chimera 1.16\share\WebServices\opal_local.py", line 156, in queryStatus
with file(statusFile) as f:
IOError: [Errno 2] No such file or directory: u'c:\\users\\doa~1\\appdata\\local\\temp\\ch2ni3mx.d\\__status'
Running AutoDock Vina for Protein_naked.pdb failed; see Reply Log for more information
Application stderr
-----
'"D:\Data\Desktop\Bioinfo_Softwares\autodock_vina_1_1_2_linux_x86\bin\vina"' is not recognized as an internal or external command,
operable program or batch file.
-----
Application stdout
-----
[no output]
-----
Please help me. How can I fix this error? (In min. 42:40)
Install exactly the softwares as i have shown in video …. As far as i can see installation properly will resolve this issue
And it will not work in windows , use Linux
Hi Dr. Dweipayan Goswami
I am Dr Mahmoud at Benha University, Egypt
I am very glad to write you
Could ask you to help me for solving troubleshooting during run the steps autodock vina.
i work on one receptor and one ligand
I face this problem:
dr@dr-G3-3579:~/docking$ vina --config -conf.txt --log log.txt
AutoDock Vina v1.2.3
Command line parse error: unrecognised option '--log'
kind regards
Mahmoud
Hi
I have explained in the same video how to modify the commad if you face the error in the following video at 26:00 ruclips.net/video/N9-HuNZthuo/видео.html