@ardhendudas8173
The most detailed video on YouTube on this topic. Thanks a lot for your effort sir.
@lumpyspaceprincess6335
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?
@krunalrambhad5596
Good explanation. I have used Combination of UCSF chimera and Pyrx for docking. Pyrx used same algorithm as autodock Vina. Only advantage I got in pyrx was it is much faster because it loads and minimised multiple Ligand in much lesser time than chimera where we individually add every ligand and save it.
@kengchiaming6471
Hi, thank you for sharing this tutorial. :) But why when I run pose1 in PLIP, the result shows no interaction?
@stromharlan5187
THANK YOU!!! This is so clearly explained.
@jeremiascorradi7865
Amazing explanation!!! thank you so much!!!
@חפירה_בקטנה
Amazing tutorial <3 Thank you very much
@tanveerhasan09
wonderful explanation using UCF Chimera. I am unable to install UCF Chimera on Linux subsystem on Windows 10. May we do docking in windows and Pymol or in Linux using PyMol. Kindly tell if possible. Still I really appreciate your lecture. Thanks May God bless you.
@945corleone
Does the resolution for the protein or receptor need to be low? If your answer is "yes", can I know why?
@alreadyghosts7727
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
@manideepgoud7122
Sir, can you explain how to run hole2 programme for protein pore calculation
@IIdogaII
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)
@mborhani-y7x
Thank you so much, it was amazing
@boorasanjit2013
respected sir, plz make video on docking by autodock tool
@Doodlemelon3004
Can I perform it at windows ?
@SITISARAHJUMALI
veryyyy useful
@Sciinsights
I have one question
@ES-yd1ze
How to do check the superimposed between original legad and and docked legand and it's impossible to to superimposed between Other
@thotavinaykumar285
Please sir, can you please do this mac os!
@ОльгаСечко-с9я