A software for multi-precision normal mode calculation of large protein assemblies
This program calculates normal modes (and many related quantities) of large protein assemblies with elastic network models.
To compile the program on a standard Unix system:
make
You should have lapack and blas installed.
To compile it with icc and using MKL: make -f nanody_linux_icc.mk
After a successful compilation,
./nanody -h
will give you a help menu.
An example run is as follows:
./nanody.exe -i 4cg4-chainA.pdb -m 0 -o 4cg4-chainA-normal-modes.nmd
The '4cg4-chainA-normal-modes.nmd' is the text output file for normal modes. It can be viewed with Network Wizard of VMD (Visual Molecular Dynamics) program.