OpenMMDL Analysis Output Files

The OpenMMDL Analysis script creates output folders and files during and after the analysis.

The following list contains a detailed overview of the folders and files: The Optional files are highlighted with an asterisk*

The following Files are generated and stored directly in the working folder where you start the OpenMMDL Analysis:

Name	Description
complex.pdb	PDB file of the protein, ligand, waters 10Å around the ligand and special ligand if selected).
df_all.csv	CSV file of the calculated interaction together with the generated fingerprints.
interactions_gathered.csv	CSV File of the calculated interaction together without the generated fingerprints.
lig.pdb	PDB file of the ligand with hydrogens.
lig.smi	Smiles file of the ligand.
ligand_numbering.png*	File that displays the ligand in 2D depiction with the correct assignment of atom numbers, which makes it easier to understand the interacting atoms.
ligand_special.pdb*	PDB file of the ligand with the special ligand.
lig_no_h.pdb	PDB file of the ligand without hydrogens.
missing_frames_filled.csv	CSV file of the calculated interactions with added frames for frames without interactions
top_10_binding_modes.csv	CSV file of the top 10 most occurring binding modes.

Barcodes

Barcodes: A folder that contains the figures of the barcodes for the interactions.

Name	Description
acceptor_interactions.png*	File displaying the barcodes for all hydrogen bond acceptor interactions.
donor_interactions.png*	File displaying the barcodes for all hydrogen bond donor interactions.
halogen_interactions.png*	File displaying the barcodes for all halogen interactions.
hydrophobic_interactions.png*	File displaying the barcodes for all hydrophobic interactions.
metal_interactions.png*	File displaying the barcodes for all metal interactions.
saltbridge_interactions.png*	File displaying the barcodes for all saltbridge interactions.
pication_interactions.png*	File displaying the barcodes for all pication interactions.
pistacking_interactions.png*	File displaying the barcodes for all pistacking interactions.
waterbridge_interactions.png*	File displaying the barcodes for all waterbridge interactions.

Binding_Modes_Markov_States

Binding_Modes_Markov_States: A folder that contains the figures of the Markov state figures and a 2D depiction figure of the top 10 occurring binding modes in addition to PDB and PML files of the representative frames of the binding modes.

Name	Description
all_binding_modes_arranged.png	Figure of the 2D depictions of the top 10 binding modes with the interacting protein partners.
Binding_mode_x.pdb	PDB File of the representative frame of the binding mode.
Binding_mode_x.pml*	PML File of the representative frame of the binding mode.
markov_chain_plot_1.png	Markov chain Figure displaying binding modes with a minimum transition of 1% of the frames between the binding modes.
markov_chain_plot_2.png	Markov chain Figure displaying binding modes with a minimum transition of 2% of the frames between the binding modes.
markov_chain_plot_5.png	Markov chain Figure displaying binding modes with a minimum transition of 5% of the frames between the binding modes.
markov_chain_plot_10.png	Markov chain Figure displaying binding modes with a minimum transition of 10% of the frames between the binding modes.

RMSD

RMSD: A folder that contains the files for the RMSD calculation during the simulation. The RMSD over time is always calculated, while the RMSD between the frames is optional.

Name	Description
RMSD_over_time.csv	CSV file with the values of the RMSD of the protein/backbone/ligand during the simulation time.
RMSD_over_time.png	Figure of the RMSD of the protein/backbone/ligand during the simulation time.
RMSD_between_the_frames.png*	Matrix figure displaying the RMSD between each consecutive frame.

Visualization

Visualization: A folder the files that are necessary for the NGLView visualization of the interactions.

Name	Description
clouds.json	JSON file that contains the information for the point clouds.
interacting_waters.dcd	Trajectory file for the point clouds visualization.
interacting_waters.pdb	Topology file for the point clouds visualization.
interacting_waters.pkl	pickle file of the interacting water ids for the point clouds visualization.