I have been trying to run Autodock Vina for my undergraduate thesis for many months have have been getting the following error. Does anyone have any ideas? I have attached an image but if that cannot be opened here is there error message through Cygwin64:
Reading input...
Parse error on line 1 in file "2jgd_DOCK.pdbqt": Unknown or inappropriate tag
mv: cannot stat 'ligand*.pdbqt': No such file or directory.
Please help!
Josie Levey
The error message "Parse error on line 1 in file '2jgd_DOCK.pdbqt" indicates an unknown or inappropriate tag. Please verify that the '2jgd_DOCK.pdbqt' file is formatted correctly to resolve this issue. You can use a tool like Open Babel to convert your files to the proper format or manually compare the errors in the Autodock Vina documentation.
To resolve the error message "mv: cannot stat 'ligand*.pdbqt': No such file or directory," please confirm that the ligand file ('ligand.pdbqt') is located in the directory where you are executing the command. If the file is in a different directory, move it to the right place or specify the correct path in your command.
Happy Docking!!
Hi Suvendu -
Thank you so much for your help. The 2jgd_DOCK file was exported from Autodock Tools in the .pdbqt format so it should be correct. I am not sure what could have gone wrong or how to change it.
The ligand.pdbqt file is in a ligand folder within the "DockingJob" folder. When I ls the folder, the ligand folder appears. Do you have any other tips for how to fix this?
Josie Levey
Hello
The error has shown, once check your notefile in which you put the grid, exhaustiveness, and all. Also, check your command line.