nmwizConverter is a simple script that takes in as command-line arguments:
- a .pdb file
- a file containing normal mode data, created using CHARMM
- the name of the molecule these files pertains to (or any other name really)
The script returns a file in .nmd format which can then be imported directly into Normal Mode Wizard, a plugin for VMD which allows researchers to visualize the vibrational modes of molecules. See http://prody.csb.pitt.edu/nmwiz/ for information on that plugin.
Anyone who understands and is interested in the above section!
This is still in alpha, so there are no frills just yet. A basic python installation is the only requirement. Python 2 & 3 both seem to work, though you'll have better luck with 3 as that's what I am developing with. Presently all one needs to do is clone this into their directory of choice and run the script as follows:
python nmwizconverter.py pdbFilename.pdb modeFilename.out moleculeName
The output file will apear in the directory in which the script was located; I intend to change this to be a user-defined location soon.
Create a new issue in the issue tracker for this git repository. I'll get to it as soon as possible since it's nice to know other people find this script useful.
Check out these sweet websites:
- NMWiz - http://prody.csb.pitt.edu/nmwiz/
- VMD - http://www.ks.uiuc.edu/Research/vmd/
- Markelz research group - http://markelz.physics.buffalo.edu