User cc45c5438e
13-08-2015 09:44:42
I have installed the ChemAxon package, however I am not able to work out the command line interface. I have been trying to follow the manual I found online, but I think i am missing some basic user info. Could anyone help?
ChemAxon d51151248d
13-08-2015 14:32:21
Hi,
Unfortunately I didn't manage to reproduce the error that you sent us. So I will give you some clues on how to run the calculation:
screen3d g filename options
The letter g refers to the generation phase of the 3D virtual screening. This step pre-processes the molecules and prepares them for the actual screening. Your molecule file can be a file that we can import. You should either put the bin directory into the PATH or use absolute paths so that the screen3d command can reach the file.
You can use the
screen3d -h
command to get full help for the command.
Daniel
User cc45c5438e
13-08-2015 14:55:47
Hi Daniel,
I tried using the -h command but the only thing I seem to be getting is another error:
Michals-MacBook-Pro:~ mzzielinski$ cd /Applications/ChemAxon/JChem/bin
Michals-MacBook-Pro:bin mzzielinski$ screen3d -h
-bash: screen3d: command not found
Michals-MacBook-Pro:bin mzzielinski$ open screen3d -h
Unable to find header file matching screen3d
Michals-MacBook-Pro:bin mzzielinski$
ChemAxon d51151248d
14-08-2015 08:46:52
Hi,
I think the path to screen3d in not in your PATH environmental variable. You should check it or re-run the JChem installer. The installer can put the bin directory in your PATH is this option is selected.
Daniel
ChemAxon 9c0afc9aaf
16-08-2015 11:08:23
Hi,
I'm not a Mac expert, but in Linux-style command-line environments usually the current directory (.) is not in the PATH either.
So once you are in the "bin" directory of JChem you should use a "./" prefix, and it should work, e.g:
./screen3d -h
Of course it's the most convenient if you add the "bin" directory of JChem to the PATH, then you can execute it from any other location as well (without the "./").
Best,
Szilard