sumner-group / dijkstra-water-wire

C++ program to find water wires linking a proton donor to acceptor in an MD simulation

dijkstra-water-wire

This is a C / C++ program for Dijkstra's single source shortest path algorithm based off of code from http://www.geeksforgeeks.org/printing-paths-dijkstras-shortest-path-algorithm/, by Aditya Goel. The code has been modified to calculate water wires connecting a donor and acceptor from an MD simulation. Currently, only Amber MD has been tested and the code can use either a pdb trajectory file or an Amber ASCII trajectory file (mdcrd). For a path to be accepted, waters must be within a user defined cutoff of each other other or of the donor or acceptor.

Input file description

filetype (mdcrd/pdb) filename number of atoms atom number for start of water chain atom number for end of water chain number of water molecules (Only for mdcrd files) distance cut-off

To compile the code

g++ -O2 -o path.exe water-wire.cpp

To run the code

./path.exe < inputfile

Sample inputs are given as input.pdb and input.mdcrd

Sample outputs are given as output.pdb and output.mdcrd

Sample mdcrd and pdb files are given as ub-nvt-step1-3.pdb and ub-nvt-step13.mdcrd. They each have three geometries.

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Anticipated updates:

1. Allowing for angles. In other words, viability also has to do with the donor-hydrogen-acceptor angle.

Do you want to cite this work?

Wilson, R. H.; Zamfir, S.; Sumner, I. “Molecular dynamics simulations reveal a new role for a conserved active site asparagine in a ubiquitin-conjugating enzyme” Journal of Molecular Graphics and Modelling, 2017, 76, 403-411. doi:10.1016/j.jmgm.2017.07.006