Protonate pdb files based on pka
propka PROPKATMP1
propka automates the protonation (positioning of hydrogen ions) to a structure in PDB format for any given pKa value. The file to use has to be named PROPKATMP1 in the directory where propka is run.
propka will generate two output files named PROPKATMP2 and PROPKATMP3. PROPKATMP2 contains the resulting structure in PDB format. PROPKATMP3 contains a summary of the propka run.
Please acknowledge your use of propka by citing:
Hui Li, Andrew D. Robertson, and Jan H. Jensen: Very Fast Empirical Prediction and Interpretation of Protein pKa Values, Proteins, 2005, 61, 704-721.
PropKa can be used via a web interface at \m[blue]http://propka.ki.ku.dk/\m[].
Manuel Prinz <[email protected]>
Wrote this manpage for the Debian System.
Copyright © 2008 Manuel Prinz