Description:

trajcontacts 1.0.1

trajcontacts
A Package for Calculating Residue-Residue Contacts from MD Trajectories
Currently, there are two modes for contact determination:


Normal Contact Analysis (norm): The presence of a contact between two residues in macromolecular systems, such as proteins and nucleic acids, is established when the minimum inter-residue heavy atom pair distance falls within a specified cutoff (4-5 Å) for a majority of the simulation time (e.g., 75% or more of snapshots). This program can be utilized to extract residue contacts from long MD simulation trajectories as well as PDB structures.


Continuous Contact Analysis (cont): As described in Botello-Smith et al., Journal of Chemical Theory and Computation 15.4 (2019): 2116-2126 and Westerlund et al., The Journal of Chemical Physics 153.14 (2020).


This is a command-line program for Linux systems and relies on the MDTraj simulation analysis package (https://www.mdtraj.org/). It uses mdtraj.load() for trajectory/topology inputs, and inter-atomic distances are calculated using mdtraj.distance(). For efficiency and to avoid memory-related errors, save the trajectories without unnecessary atoms (solvent/ions or hydrogen atoms) and divide the trajectory into multiple chunks, then write their names (or pathnames) in a file (for example, name that file 'traj.dat') - see below.
Installation
You can install trajcontacts by running:
pip install trajcontacts
After installation, you can access detailed options by typing:
trajcontacts -h
For a simple usage example, running the following command:
trajcontacts -p topologyfile -f file_containing_names/paths_to_coordinate_files -n 10
will execute the program on 10 processors and extract contacts with a 4.5 Ångstrom cutoff. Both 'topologyfile' (specified in the command line) and 'coordinatefile' (in the file containing names of coordinate files) should be specified as the same for extracting contacts from a PDB file.
Example
trajcontacts -p 3sn6.pdb -f traj.dat -n 10
where 'traj.dat' is a file with a single line containing '3sn6.pdb'.
How to Cite:
Please cite the following research when using trajcontacts:
Madhu, Midhun K., Kunal Shewani, and Rajesh K. Murarka. "Biased Signaling in Mutated Variants of β2-Adrenergic Receptor: Insights from Molecular Dynamics Simulations." bioRxiv (2023): 2023-09.
Copyright:
Copyright belongs to the Computational Biophysics and Soft Matter Group, IISER Bhopal. Visit our website: https://home.iiserb.ac.in/~rkm/.

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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