EP 1 | MOLECULAR DOCKING in UCSF CHIMERA by VINA Plugin from Scratch in Linux

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I am Dr. Dweipayan Goswami,
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Key links
UCSF CHIMERA : www.cgl.ucsf.e...
AutoDock Vina Download : vina.scripps.e...

[@user-im7zf7ei1n]

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!

[@ardhendudas8173]

The most detailed video on KZbin on this topic. Thanks a lot for your effort sir.

[@stromharlan5187]

THANK YOU!!! This is so clearly explained.

[@jeremiascorradi7865]

Amazing explanation!!! thank you so much!!!

[@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

[@user-qo8el3ri6h]

Thank you so much, it was amazing

[@rafathossain5845]

Vai awesome

[@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?

[@user-cz9qn9gs4p]

veryyyy useful

[@manideepgoud7122]

Sir, can you explain how to run hole2 programme for protein pore calculation

[@945corleone]

Does the resolution for the protein or receptor need to be low? If your answer is "yes", can I know why?

[@boorasanjit2013]

respected sir, plz make video on docking by autodock tool

[@Arya_stark_95]

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

[@DweipayanG]

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 .

[@Arya_stark_95]

@@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??

[@ShivamGupta-uj4jf]

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

[@DweipayanG]

There might be some error in steps performed..

[@Sciinsights]

I have one question

[@MahendraSingh-ge5wz]

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?

[@DweipayanG]

Ligand file has to be a .mol2 file

[@MahendraSingh-ge5wz]

@@DweipayanG Sir, alreday did as per your guidelines but at the end i got the error.

[@MahendraSingh-ge5wz]

@@DweipayanG i got two files protein.mol2 and ligand.mol2 both were run through chimera- autodockvina after "apply" key get error prompt

[@DweipayanG]

In the last step i guess u have chosen protein as ligand and ligand as receptor in the top part of vinna panel !

[@MahendraSingh-ge5wz]

@@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.

[@thotavinaykumar285]

Please sir, can you please do this mac os!

[@PriyankaKumari-ig2ok]

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

[@DweipayanG]

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

[@dogal.5642]

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)

[@DweipayanG]

Install exactly the softwares as i have shown in video …. As far as i can see installation properly will resolve this issue

[@DweipayanG]

And it will not work in windows , use Linux

[@YaNaBiology3004]

Can I perform it at windows ?

[@ES-yd1ze]

How to do check the superimposed between original legad and and docked legand and it's impossible to to superimposed between Other

[@DweipayanG]

Its possible in ucsf chimera and i have shown that in my videos too how to do that …

[@ES-yd1ze]

​@@DweipayanG If that occur that means the docked ligand and co-crystalized ligand are same ??

[@ES-yd1ze]

​@@DweipayanG I see your co cryslazed ligand and docked ligand are same ? Please explain sir

[@mahmoudmustafa2805]

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

[@DweipayanG]

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 kzbin.info/www/bejne/hGqQeaiEj9mbq9E