Quick usage

If you created a conda environment to use GPathFinder (as proposed in installation), first you need to activate it with:

conda activate name_of_the_environment

or

source activate name_of_the_environment

Running GAUDI jobs is quite easy with gaudi.cli.gaudi_run. Put in your terminal:

gpath run /path/to/input_file.yaml

You will need at least three input files. A .yaml file with the configuration of the job and two .mol2 files for the ligand and the receptor molecules. To learn how to create input files, go to Input files. You can also check the tutorials Understanding the different sections of the input file and Preparing ligand and protein files.

After the job is completed, you can use our home-made scripts to analyze them. A complete description of the output files is provided in Output files, and some tutorials on how to perform different analysis are available in Analyzing GPathFinder results.

To understand better the complete process of a GPathFinder calculation, you have also available the tutorial Your first GPathFinder calculation.