#include "utilities.txt"

$homedir = "/home/aroop" ;

$rosettadir = "$homedir/simcode" ;

$basedir = "$rosettadir/antibody" ;

$jobdir = "$basedir/jobs" ;

$scripts = "$basedir/scripts" ;

$scripts_alt = "$rosettadir/rosetta_scripts/docking/pdb_scripts" ;

$docking_scripts = "$rosettadir/rosetta_scripts/docking";

$pdbfiles = "$basedir/pdbfiles" ;

$renumbered = "$pdbfiles/renumbered" ;

$idealized = "$pdbfiles/idealized" ;

$idealizedL = "$pdbfiles/idealizedL" ;

$idealizedH = "$pdbfiles/idealizedH" ;

$info = "$basedir/info" ;

$database = "$basedir/database" ;

$testset = "$basedir/testset" ;

$blast = "$homedir/simcode/shareware/blast2.2.12" ;

$dsspfiles = "$basedir/dsspfiles" ;

$fragments = "$basedir/fragments" ;

$WAMmodels = "$basedir/WAMmodels" ;

$bin = "$rosettadir/rosetta++" ;

$misc = "$docking_scripts/condor_scripts" ;

$kink = "$basedir/kink" ;

$hbondfiles = "$basedir/hbondfiles" ;

$abfrags = "$basedir/abfrags" ;

$rosettafrags = "$basedir/rosettafrags" ;

$structures = "$basedir/structures" ;
