Torsional Network Model (TNM) program

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.

本压缩包包含编译并运行扭转网络模型（torsional network model，TNM）程序所需的全部文件。该程序可在扭转角空间中计算输入蛋白质的简正模式，并利用这些简正模式完成三项任务：生成备选蛋白质结构、分析构象变化（若提供第二份结构作为输入），以及计算蛋白质残基与功能位点间的动态耦合作用。
该程序可计算PDB（Protein Data Bank）文件<pdb1>的链<chain1>（默认取第一条链）的TNM模式，并将<nmodes>（默认值为0）个最低频简正模式以多PDB文件、扭转角分量及笛卡尔坐标分量的形式输出。若提供<pdb2>，程序将把从<pdb1>到<pdb2>的构象变化投影至<pdb1>的简正模式空间，同时生成名为Summary_<....>.dat的投影总结文件，以及存储逐模式投影结果的<...>Modes.dat文件。