(c) Thomas Haschka 2009-2022
A tool to perform quick normal mode analysis on a PDB file according to the method first proposed by Tirion et al..
Please cite:
This tool now has a youtube tutorial: https://youtu.be/jUBWMLQYkKk
The program was almost completely ( by exercise ) written using the SSE2 + SSSE3 intrinsics, and as such requires an intel/amd processor supporting these instructions to work. Anything built after 2008 basically should do it.
The program further needs the lapack libraries. On a contemporary Debian Based system you should be able to obtain all requirements using:
sudo apt-get install build-essential liblapack-dev
You can then compile the program:
gcc -O2 -march=native nma-double.c -o nma -lm -llapack
obtaining the nma binary.
The nma tool is pretty self explanatory. Its arguments are:
file: pdb file
k: spring constant in atom - atom interaction potential
cut: Cutoff of atom - atom interaction in Angstr.
nmax: highest mode to be visualized. nmax has to satisfy
7 < nmax < 100
in example if you download the PDB file 1uqq you may perform nma analysis in typing:
./nma 1quu.pdb pdb 0.5 15 9
which should yield the files:
7-mode.xyz
8-mode.xyz
9-mode.xyz
eigenvalues
The eigenvalues give you an idea of how much each mode should get occupied as the protein gets excited. Each mode can be visualized for instance with VMD using the Van der Waals representation in this program you might get nice movies of each mode.
The program was in its original form written in 2009 as part of Thomas Haschka's Master Theses