Thanks @Bioinforphile for this excellent video. However, when I tried the step, I get to a point with an error saying "Error: could not open "conf_vs.txt" for reading. Can you help?
In AutoDock Vina, the "Spacing" parameter in the configuration file (conf.txt) specifies the spacing (grid spacing) between grid points in the grid box used for docking. This parameter determines the resolution of the grid, which affects the accuracy and speed of the docking calculations. The default value used by AutoDock Vina is 1 Ångstrom. f the conf_vs.txt file generated by AutoDock Vina does not contain the Spacing parameter, you can add it manually to the configuration file (conf.txt). Typically, the Spacing parameter is set to a value between 0.375 Ångstrom and 1 Ångstrom. spacing = 1.0
Output will be 10_out.pdbqt Detected 4 CPUs Reading input ... Error: could not open "receptor.pdbqt" for reading. i am getting this error kindly help me. what to do
This part of the error message indicates that the software is encountering an issue related to the size of the search space volume specified for docking. AutoDock Vina has a limit on the size of the search space volume, and it seems that the specified volume exceeds this limit (which is set to 2700 Angstrom^3). You may need to adjust the size of your search space to be within this limit.
I learned a lot by following your channel, keep on sharing!
Thank you for your encouraging words.
Awesome Video.... Thanks for help
Thanks for informative tutorial.
Thanks @Bioinforphile for this excellent video. However, when I tried the step, I get to a point with an error saying "Error: could not open "conf_vs.txt" for reading. Can you help?
I've solved it. Working now. Thanks
There may be an error in the file path. Please check.
The conf_vs.txt does not contain the Spacing (anstrom). How can I add it and what is it basically set to? Thanks.
In AutoDock Vina, the "Spacing" parameter in the configuration file (conf.txt) specifies the spacing (grid spacing) between grid points in the grid box used for docking. This parameter determines the resolution of the grid, which affects the accuracy and speed of the docking calculations. The default value used by AutoDock Vina is 1 Ångstrom. f the conf_vs.txt file generated by AutoDock Vina does not contain the Spacing parameter, you can add it manually to the configuration file (conf.txt). Typically, the Spacing parameter is set to a value between 0.375 Ångstrom and 1 Ångstrom. spacing = 1.0
I keep getting the error ,command line parse error: unrecognized option. ‘-log’
Output will be 10_out.pdbqt
Detected 4 CPUs
Reading input ...
Error: could not open "receptor.pdbqt" for reading. i am getting this error kindly help me. what to do
Getting error space volume > 2700 Angstrom 3
Could not open receptor. Pdbqt
This part of the error message indicates that the software is encountering an issue related to the size of the search space volume specified for docking. AutoDock Vina has a limit on the size of the search space volume, and it seems that the specified volume exceeds this limit (which is set to 2700 Angstrom^3). You may need to adjust the size of your search space to be within this limit.