Torsional Network Model (TNM) program

Published: 16-11-2018| Version 1 | DOI: 10.17632/6x65mphr25.1
Ugo Bastolla


zip package with all files necessary for compiling and executing the tnm (torsional network model) program that computes the normal modes of an input protein in the space of torsion angles and uses these normal modes for generating alternative structures, analysing a conformation change (if a second structure is provided as input) and computing dynamic couplings between residues and between functional sites of the protein. The program computes tnm modes of chain(s) <chain1> (default: first chain) of pdb file <pdb1> and prints the <nmodes> (default: 0) lowest modes in multi-pdb files and as torsional and cartesian components. If <pdb2> is provided, the program projects the conformation change from <pdb1> to <pdb2> onto the normal modes of <pdb1> and outputs a summary of the projection in a file called Summary_<....>.dat and mode by mode projections in <...>Modes.dat.


Steps to reproduce

To compile, please save into your chosen installation directory and run >unzip >make (you may want to change the compilation options in the Makefile) >cp tnm /bin/ (copy to a binary files directory contained in your PATH, as specified for instance in the ~/.tcshrc file) RUNNING WITH CONFIGURATION FILE (RECOMMENDED) ============================================= >./tnm A template configuration file is provided in the archive. The main records are explained there.