Running MDPath

This page details the primary functionality of MDPath, which is the analysis of signaling pathways in proteins based on molecular dynamics simulations.

Usage

To use the main function of MDPath, always use the prefix mdpath followed by the corresponding mandatory and optional flags.

Mandatory Inputs

The following inputs are required when running MDPath from the command line:

-top    Topology file of your molecular dynamics simulation [.pdb]
-traj   Trajectory file of your molecular dynamics simulation [.dcd]

Optional Inputs In addition to the mandatory inputs, the following optional parameters can be provided to customize the analysis:

-cpu       Number of virtual cores to use [n]
-lig       Important residues a path must cross in order to be plotted [list of residues, e.g.: 1 2 3 4 ... (**Important!** No commas and no square brackets)]
-bs        Number of bootstrap samples to be calculated for your system [n]
-fardist   Minimum distance in angstroms for residues to be considered as start and end points for pathways [n]
-closedist Minimum distance in angstroms for residues to be considered overlapping for clustering [n]
-graphdist Minimum distance in angstroms for residues to be considered to have corresponding movements for graph building [n]
-numpath   Number of top paths with the highest normalized mutual information to be plotted [n]
-digamma_correction   Apply the digamma correction to the mutual information calculation [True/False]
-GMM      Create histograms for the mutual information calculation based on Gaussian mixture models [True/False]
-chain    Chain of the protein to be analyzed [chain ID]
-invert   Inverts NMI bei subtrackting each NMI from max NMI. Can be used to find Paths, that are the least correlated [True/False]

An example command line input for running MDPath could look like this:

mdpath -top [Path to your topology].pdb -traj [Path to your trajectory].dcd