# Starting log file on Tue Sep 30 16:46:15 EDT 2014
#
# The following are the commands used to generate the ptraj/cpptraj-generated 
# coordinate analysis data in this directory.
# 

 /programs/amber12/bin/cpptraj -i TESTBRIDGE/PhiPsi_TEST_all_frames_NoWAT_1_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/Karplus_TEST_all_frames_NoWAT_1_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/ptraj ../input/Single.parm7 < TESTBRIDGE/Distance_TEST_all_frames_NoWAT_1_cpptraj.in 
 paste TESTBRIDGE/Distance_H-H_TEST_all_frames_NoWAT_1_cpptraj.out TESTBRIDGE/Distance_O-O_TEST_all_frames_NoWAT_1_cpptraj.out > TESTBRIDGE/Distance_HH+OO_TEST_all_frames_NoWAT_1_cpptraj.out 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/PhiPsi_TEST_all_frames_NoWAT_2_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/Karplus_TEST_all_frames_NoWAT_2_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/ptraj ../input/Single.parm7 < TESTBRIDGE/Distance_TEST_all_frames_NoWAT_2_cpptraj.in 
 paste TESTBRIDGE/Distance_H-H_TEST_all_frames_NoWAT_2_cpptraj.out TESTBRIDGE/Distance_O-O_TEST_all_frames_NoWAT_2_cpptraj.out > TESTBRIDGE/Distance_HH+OO_TEST_all_frames_NoWAT_2_cpptraj.out 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/PhiPsi_TEST_all_frames_NoWAT_3_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/Karplus_TEST_all_frames_NoWAT_3_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/ptraj ../input/Single.parm7 < TESTBRIDGE/Distance_TEST_all_frames_NoWAT_3_cpptraj.in 
 paste TESTBRIDGE/Distance_H-H_TEST_all_frames_NoWAT_3_cpptraj.out TESTBRIDGE/Distance_O-O_TEST_all_frames_NoWAT_3_cpptraj.out > TESTBRIDGE/Distance_HH+OO_TEST_all_frames_NoWAT_3_cpptraj.out 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/PhiPsi_TEST_all_frames_NoWAT_4_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/Karplus_TEST_all_frames_NoWAT_4_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/ptraj ../input/Single.parm7 < TESTBRIDGE/Distance_TEST_all_frames_NoWAT_4_cpptraj.in 
 paste TESTBRIDGE/Distance_H-H_TEST_all_frames_NoWAT_4_cpptraj.out TESTBRIDGE/Distance_O-O_TEST_all_frames_NoWAT_4_cpptraj.out > TESTBRIDGE/Distance_HH+OO_TEST_all_frames_NoWAT_4_cpptraj.out 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/PhiPsi_TEST_4Ways_1_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/Karplus_TEST_4Ways_1_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/ptraj ../input/Single.parm7 < TESTBRIDGE/Distance_TEST_4Ways_1_cpptraj.in 
 paste TESTBRIDGE/Distance_H-H_TEST_4Ways_1_cpptraj.out TESTBRIDGE/Distance_O-O_TEST_4Ways_1_cpptraj.out > TESTBRIDGE/Distance_HH+OO_TEST_4Ways_1_cpptraj.out 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/PhiPsi_TEST_4Ways_2_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/Karplus_TEST_4Ways_2_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/ptraj ../input/Single.parm7 < TESTBRIDGE/Distance_TEST_4Ways_2_cpptraj.in 
 paste TESTBRIDGE/Distance_H-H_TEST_4Ways_2_cpptraj.out TESTBRIDGE/Distance_O-O_TEST_4Ways_2_cpptraj.out > TESTBRIDGE/Distance_HH+OO_TEST_4Ways_2_cpptraj.out 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/PhiPsi_TEST_4Ways_3_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/Karplus_TEST_4Ways_3_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/ptraj ../input/Single.parm7 < TESTBRIDGE/Distance_TEST_4Ways_3_cpptraj.in 
 paste TESTBRIDGE/Distance_H-H_TEST_4Ways_3_cpptraj.out TESTBRIDGE/Distance_O-O_TEST_4Ways_3_cpptraj.out > TESTBRIDGE/Distance_HH+OO_TEST_4Ways_3_cpptraj.out 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/PhiPsi_TEST_4Ways_4_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/Karplus_TEST_4Ways_4_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/ptraj ../input/Single.parm7 < TESTBRIDGE/Distance_TEST_4Ways_4_cpptraj.in 
 paste TESTBRIDGE/Distance_H-H_TEST_4Ways_4_cpptraj.out TESTBRIDGE/Distance_O-O_TEST_4Ways_4_cpptraj.out > TESTBRIDGE/Distance_HH+OO_TEST_4Ways_4_cpptraj.out 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/PhiPsi_TEST_4Way-noBridge_1_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/Karplus_TEST_4Way-noBridge_1_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/ptraj ../input/Single.parm7 < TESTBRIDGE/Distance_TEST_4Way-noBridge_1_cpptraj.in 
 paste TESTBRIDGE/Distance_H-H_TEST_4Way-noBridge_1_cpptraj.out TESTBRIDGE/Distance_O-O_TEST_4Way-noBridge_1_cpptraj.out > TESTBRIDGE/Distance_HH+OO_TEST_4Way-noBridge_1_cpptraj.out 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/PhiPsi_TEST_4Way-noBridge_2_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/Karplus_TEST_4Way-noBridge_2_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/ptraj ../input/Single.parm7 < TESTBRIDGE/Distance_TEST_4Way-noBridge_2_cpptraj.in 
 paste TESTBRIDGE/Distance_H-H_TEST_4Way-noBridge_2_cpptraj.out TESTBRIDGE/Distance_O-O_TEST_4Way-noBridge_2_cpptraj.out > TESTBRIDGE/Distance_HH+OO_TEST_4Way-noBridge_2_cpptraj.out 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/PhiPsi_TEST_4Way-noBridge_3_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/Karplus_TEST_4Way-noBridge_3_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/ptraj ../input/Single.parm7 < TESTBRIDGE/Distance_TEST_4Way-noBridge_3_cpptraj.in 
 paste TESTBRIDGE/Distance_H-H_TEST_4Way-noBridge_3_cpptraj.out TESTBRIDGE/Distance_O-O_TEST_4Way-noBridge_3_cpptraj.out > TESTBRIDGE/Distance_HH+OO_TEST_4Way-noBridge_3_cpptraj.out 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/PhiPsi_TEST_4Way-noBridge_4_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/Karplus_TEST_4Way-noBridge_4_cpptraj.in -p ../input/Single.parm7 
 /programs/amber12/bin/ptraj ../input/Single.parm7 < TESTBRIDGE/Distance_TEST_4Way-noBridge_4_cpptraj.in 
 paste TESTBRIDGE/Distance_H-H_TEST_4Way-noBridge_4_cpptraj.out TESTBRIDGE/Distance_O-O_TEST_4Way-noBridge_4_cpptraj.out > TESTBRIDGE/Distance_HH+OO_TEST_4Way-noBridge_4_cpptraj.out 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/PhiPsi_TEST_Bridge_bonds_1_cpptraj.in -p ../input/plus1water.parm7 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/Karplus_TEST_Bridge_bonds_1_cpptraj.in -p ../input/plus1water.parm7 
 /programs/amber12/bin/ptraj ../input/plus1water.parm7 < TESTBRIDGE/Distance_TEST_Bridge_bonds_1_cpptraj.in 
 paste TESTBRIDGE/Distance_H-H_TEST_Bridge_bonds_1_cpptraj.out TESTBRIDGE/Distance_O-O_TEST_Bridge_bonds_1_cpptraj.out > TESTBRIDGE/Distance_HH+OO_TEST_Bridge_bonds_1_cpptraj.out 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/PhiPsi_TEST_Bridge_bonds_2_cpptraj.in -p ../input/plus1water.parm7 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/Karplus_TEST_Bridge_bonds_2_cpptraj.in -p ../input/plus1water.parm7 
 /programs/amber12/bin/ptraj ../input/plus1water.parm7 < TESTBRIDGE/Distance_TEST_Bridge_bonds_2_cpptraj.in 
 paste TESTBRIDGE/Distance_H-H_TEST_Bridge_bonds_2_cpptraj.out TESTBRIDGE/Distance_O-O_TEST_Bridge_bonds_2_cpptraj.out > TESTBRIDGE/Distance_HH+OO_TEST_Bridge_bonds_2_cpptraj.out 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/PhiPsi_TEST_Bridge_bonds_3_cpptraj.in -p ../input/plus1water.parm7 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/Karplus_TEST_Bridge_bonds_3_cpptraj.in -p ../input/plus1water.parm7 
 /programs/amber12/bin/ptraj ../input/plus1water.parm7 < TESTBRIDGE/Distance_TEST_Bridge_bonds_3_cpptraj.in 
 paste TESTBRIDGE/Distance_H-H_TEST_Bridge_bonds_3_cpptraj.out TESTBRIDGE/Distance_O-O_TEST_Bridge_bonds_3_cpptraj.out > TESTBRIDGE/Distance_HH+OO_TEST_Bridge_bonds_3_cpptraj.out 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/PhiPsi_TEST_Bridge_bonds_4_cpptraj.in -p ../input/plus1water.parm7 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/Karplus_TEST_Bridge_bonds_4_cpptraj.in -p ../input/plus1water.parm7 
 /programs/amber12/bin/ptraj ../input/plus1water.parm7 < TESTBRIDGE/Distance_TEST_Bridge_bonds_4_cpptraj.in 
 paste TESTBRIDGE/Distance_H-H_TEST_Bridge_bonds_4_cpptraj.out TESTBRIDGE/Distance_O-O_TEST_Bridge_bonds_4_cpptraj.out > TESTBRIDGE/Distance_HH+OO_TEST_Bridge_bonds_4_cpptraj.out 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/PhiPsi_TEST_Bridge-no4Way_1_cpptraj.in -p ../input/plus1water.parm7 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/Karplus_TEST_Bridge-no4Way_1_cpptraj.in -p ../input/plus1water.parm7 
 /programs/amber12/bin/ptraj ../input/plus1water.parm7 < TESTBRIDGE/Distance_TEST_Bridge-no4Way_1_cpptraj.in 
 paste TESTBRIDGE/Distance_H-H_TEST_Bridge-no4Way_1_cpptraj.out TESTBRIDGE/Distance_O-O_TEST_Bridge-no4Way_1_cpptraj.out > TESTBRIDGE/Distance_HH+OO_TEST_Bridge-no4Way_1_cpptraj.out 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/PhiPsi_TEST_Bridge-no4Way_2_cpptraj.in -p ../input/plus1water.parm7 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/Karplus_TEST_Bridge-no4Way_2_cpptraj.in -p ../input/plus1water.parm7 
 /programs/amber12/bin/ptraj ../input/plus1water.parm7 < TESTBRIDGE/Distance_TEST_Bridge-no4Way_2_cpptraj.in 
 paste TESTBRIDGE/Distance_H-H_TEST_Bridge-no4Way_2_cpptraj.out TESTBRIDGE/Distance_O-O_TEST_Bridge-no4Way_2_cpptraj.out > TESTBRIDGE/Distance_HH+OO_TEST_Bridge-no4Way_2_cpptraj.out 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/PhiPsi_TEST_Bridge-no4Way_3_cpptraj.in -p ../input/plus1water.parm7 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/Karplus_TEST_Bridge-no4Way_3_cpptraj.in -p ../input/plus1water.parm7 
 /programs/amber12/bin/ptraj ../input/plus1water.parm7 < TESTBRIDGE/Distance_TEST_Bridge-no4Way_3_cpptraj.in 
 paste TESTBRIDGE/Distance_H-H_TEST_Bridge-no4Way_3_cpptraj.out TESTBRIDGE/Distance_O-O_TEST_Bridge-no4Way_3_cpptraj.out > TESTBRIDGE/Distance_HH+OO_TEST_Bridge-no4Way_3_cpptraj.out 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/PhiPsi_TEST_Bridge-no4Way_4_cpptraj.in -p ../input/plus1water.parm7 
 /programs/amber12/bin/cpptraj -i TESTBRIDGE/Karplus_TEST_Bridge-no4Way_4_cpptraj.in -p ../input/plus1water.parm7 
 /programs/amber12/bin/ptraj ../input/plus1water.parm7 < TESTBRIDGE/Distance_TEST_Bridge-no4Way_4_cpptraj.in 
 paste TESTBRIDGE/Distance_H-H_TEST_Bridge-no4Way_4_cpptraj.out TESTBRIDGE/Distance_O-O_TEST_Bridge-no4Way_4_cpptraj.out > TESTBRIDGE/Distance_HH+OO_TEST_Bridge-no4Way_4_cpptraj.out