Understanding the output files

Folder structure

Each time you launch a new simulation, the Platform will generate a top level directory including all input and output files.

Unless you provide a custom folder name using working_folder parameters, it will automatically enumerate one based on the name of the perturbed ligand, e.g. LIG_Pele, LIG_Pele_1, etc. ensuring the old simulations will not be overwritten.

.
└── LIG_Pele
    ├── Data
    ├── DataLocal
    ├── Documents
    ├── input
    ├── output
    └── results
        ├── top_poses
        ├── plots
        └── clusters

Top level directory

The top level directory contains the logs, configuration files and a copy of input.yaml created by the user.

  • LIG.log: log file

  • adaptive.conf: control file for AdaptivePELE (learn more)

  • input.yaml: user’s configuration file

  • pele.conf: control file for PELE (learn more)

  • LIG.mae: the rotamer library

Additionally, it contains several Data and Documents folder required by PELE++, which contain residue templates and rotamer libraries. More details here.

Input

The input folded contains:

  • system_preprocessed.pdb: original PDB file preprocessed by the Platform

  • input*.pdb: input files with initial poses (depends on the package)

  • receptor.pdb: PDB file with extracted protein

  • ligand.pdb: PDB file with extracted ligand.

Output

Most importantly, this directory contains raw PELE output, i.e. report and trajectory files containing every step of the simulation, split into several folders, depending on the number of iterations performed.

Additionally, you will find information about topologies and clustering performed by AdaptivePELE.

Results

The results directory holds a more user-friendly, curated output comprising of three separate folders:

  • top_poses - top 100 lowest binding energy structures, unless the user specified a different number of top poses to be extracted

  • plots - plots of multiple metrics selected by the user (such as SASA or atom distance), providing an insight into the progress of the simulation

  • clusters - lowest binding energy cluster representatives (unless the user specified a different metric) and clustering plots.