Charmm requires a patch to recognize that nitrogenous bases are deoxy versus oxy. This parser outputs the various residues that require a patch by identifying those atoms in nitrogenous bases that do not have a coordinate for their respective O2' oxygens.
Syntax: python R2Dparser.py ~/Location/outputFileName *Replace Location with location of the output file from charmm that lists the residues needing to be converted
Output: a file named patch.out with the patch expressions for in xrange(1,10): pass atoms from RNA to DNA
Note!!!: The outputFile from charmm must be contain the command coor print for this script to read corretly.
Written by: Connor Fourt Last Updated: May 23 2014 Written: May 23 2014