Interaction analysis for molecular structures and ensembles

Computing contact fingerprints from multiple MD simulations

The following steps will generate a contact fingerprint for a set of static structures (e.g. PDB-files solved with X-ray crystallography).

Assume you have two simulations of different molecules represented with the following topology and trajectory files:

For each trajectory we first generate a contact list and then set of residue contact frequencies: --topology top_1.pdb --trajectory trj_1.dcd --itypes hb --output contacts_1.tsv --topology top_2.pdb --trajectory trj_2.dcd --itypes hb --output contacts_2.tsv --input_files contacts_1.tsv --output_file resfrequencies_1.tsv --input_files contacts_2.tsv --output_file resfrequencies_2.tsv

Next, the residue contact frequencies are combined a plot is written to a png file: --input_frequencies resfrequencies_1.tsv resfrequencies_2.tsv \
                              --column_headers Sim1 Sim2 \
                              --frequency_cutoff 0.6 \
                              --plot_output fingerprint.png