I think Maciej did a great job with this, but in case it's helpful, I made a supplemental video where I basically just follow along with Maciej's tutorial and show the menu selections in more detail: th-cam.com/video/8I1BP201yLQ/w-d-xo.html
@@GianmarcGrazioliPhD Thank you very much! I'm also having a hard time to understand this video because can't see what exactly he's clicking. Yours is very helpful
Thanks for this video, how can you control the box size ? I tried to click on ctrl and 2 with continues pushing on left click but didn't get any boxes !? Can you explain?
Thank you for an informative tutorial. Please could you tell me why I get two sets of docking results when I only have one protein and one ligand? I get one set on pressing apply and different set on pressing ok in the set-up dialogue box. What is the difference between the two sets of results? (The energies are not the same).
Hi, nice video. I have a question, I've seen tutorials of how to do docking and sometimes they use the option Dock Prep before to use the tool autodock vina, for prepare protein, ligand and assign charges, which option is the correct? or is the same? Thanks.
Dock Prep is used for docking using DOCK software. Dock Prep performs several tasks to prepare structures for DOCK or for other calculations, such as: -deleting water molecules -repairing truncated sidechains -adding hydrogens -assigning partial charges -writing files in Mol2 format So if your model needs some "cleanup" you can go ahead and use it.
Hi Dr Macienj, I'm performing molecular docking using Chimera app and Autodock Vina on Mac OS. The protein I open in Chimera has selenocysteine in it's active site, and it's avoiding me to do the docking, showing the following error: "The geometries and expected number of substituents for some atoms in the current models are unknown. These atoms are listed below. For each, please indicate the expected geometry and number of substituents. When done, click 'OK'." What should I do to fix this problem
Try using Tools -> Surface/Binding Analysis -> Dock Prep and run default settings (with "Incomplete side chains" checked) on the receptor before running the docking analysis
After a box has been created, it can be erased or further adjusted. Clicking the assigned button at a point not over the box erases the box. Dragging from a point over the box moves the frontmost face; also holding down Shift moves the the rearmost face instead of the frontmost. Dragging from a point not over the box translates the whole box in X and Y; Shift-dragging translates the box in the Z dimension. www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html
When you download AutoDock Vina, the program is automatically stored in a file called "The Scripps Research Institute." If you are using Windows 64, that will be found under "C:\Program Files (x86)\The Scripps Research Institute". You can move the program file to any other file location that you want.
This is very helpful, thanks a lot for posting this!
what is this, why is your screen cut, I don't even know what you are pressing
I think Maciej did a great job with this, but in case it's helpful, I made a supplemental video where I basically just follow along with Maciej's tutorial and show the menu selections in more detail: th-cam.com/video/8I1BP201yLQ/w-d-xo.html
@@GianmarcGrazioliPhD Thank you very much! I'm also having a hard time to understand this video because can't see what exactly he's clicking. Yours is very helpful
Thank you for the tutorial. Please, how were you able to move the box independently.
Hello thanks for your video
Is it different using autodock tools and chimera??
I got different result from using ADT and chimera..
hello, did u manage to get the answer for this? I am using chimera bus auto dock tools cannot run on my laptop
Why you are not adding charges and hydrogen atoms to ligands and protein before docking.
Thanks for this video, how can you control the box size ? I tried to click on ctrl and 2 with continues pushing on left click but didn't get any boxes !? Can you explain?
I have the same problem, you can try "Ctrl button 1" or "button 1" mode. I found it effective in my case
Thank you for this informative tutorial. Is it possible do high throughput VS screening using vina Chimera.
very informative.
Can you please suggest why after docking i am getting two posses of the ligand at the binding site
It is mean that before we conducted spesifik docking we have to blind docking first, right?
Thank you for an informative tutorial. Please could you tell me why I get two sets of docking results when I only have one protein and one ligand? I get one set on pressing apply and different set on pressing ok in the set-up dialogue box. What is the difference between the two sets of results? (The energies are not the same).
how did you selected only benzamidin reside that is not clear and not visible path. kindly help me in this regard.
How can i calculate delta G with chimera?
Hi, nice video. I have a question, I've seen tutorials of how to do docking and sometimes they use the option Dock Prep before to use the tool autodock vina, for prepare protein, ligand and assign charges, which option is the correct? or is the same? Thanks.
Dock Prep is used for docking using DOCK software. Dock Prep performs several tasks to prepare structures for DOCK or for other calculations, such as:
-deleting water molecules
-repairing truncated sidechains
-adding hydrogens
-assigning partial charges
-writing files in Mol2 format
So if your model needs some "cleanup" you can go ahead and use it.
Hi Dr Macienj, I'm performing molecular docking using Chimera app and Autodock Vina on Mac OS. The protein I open in Chimera has selenocysteine in it's active site, and it's avoiding me to do the docking, showing the following error:
"The geometries and expected number of substituents for some atoms in the current models are unknown. These atoms are listed below. For each, please indicate the expected geometry and number of substituents. When done, click 'OK'."
What should I do to fix this problem
Hi, i had the same problem, did you can fix it?? Please i apreciate your help
Try using Tools -> Surface/Binding Analysis -> Dock Prep and run default settings (with "Incomplete side chains" checked) on the receptor before running the docking analysis
Please can you help me with how to draw a grid box. I am not clear with that step
After a box has been created, it can be erased or further adjusted.
Clicking the assigned button at a point not over the box erases the box.
Dragging from a point over the box moves the frontmost face; also holding down Shift moves the the rearmost face instead of the frontmost.
Dragging from a point not over the box translates the whole box in X and Y; Shift-dragging translates the box in the Z dimension.
www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html
can you please tell me how to find my executable location for auto dock vina ??
the scripps research institute/vina
When you download AutoDock Vina, the program is automatically stored in a file called "The Scripps Research Institute." If you are using Windows 64, that will be found under "C:\Program Files (x86)\The Scripps Research Institute". You can move the program file to any other file location that you want.
I dont think he is doing the right thing. He has neither added hdyrogen atoms nor distributed the charges which can be done using chimera
How does the program determine where the protein is positioned relative to the receptor?
It does not. You can manipulate if freely.