Hello,
I am conducting a protein-metal docking in Autodock using an Arsenic compound and am unable to produce a proper GLG file. When I complete the autogrid I get the following error in the GLG file:
GPF> parameter_file AD4.1_bound.dat
Using read_parameter_library() to try to open and read "AD4.1_bound.dat".
/autogrid4.exe: FATAL ERROR: Sorry, I can't find or open AD4.1_bound.dat
/autogrid4.exe: Unsuccessful Completion.
I am unsure if the problem comes from an issue with the software, parameter file, or even python? The python shell shows some errors, but I don't know if that is just because the parameterization was unsuccessful.
To solve the issue I have tried the following steps but they did not fix the error:
- After setting up grid, Output>Save GPF>”File.gpf”. Then opening up the File.gpf in the folder and adding “parameter_file AD4.1_bound.dat” to the very first line.
- After saving the grid, selecting Other Options>Parameter Library Filename>Select file>Edit Parameter Library>Select File>OK>Output>Save GPF>”File.gpf” to directly add the parameter file to the GPF file using Autodock
- Copying the parameter files from the vina website and adding only additional atoms of interest
- No spaces in files/pathways and ensuring everything in the same workspace folder
- Unchecked Read-only from properties of folder
- Ran Autodock Tools as an administrator
- Set "Startup Directory" as "C:\Workspace" from AutoDock Tools preferences.
Thank you very much.
Tutorial on how to incorporate easily a custom AD4 parameter file when using Autodock4
https://github.com/Valdes-Tresanco-MS/AMDock-win/wiki/4.5.3-Input-a-customized-AD4-parameter-file
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