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Py

#################
# JOB VARIABLES #
#################

start_expt = 1
end_expt = 32

start_analysis_frame = 2000

par_dir = '/mindstore/home33ext/kscopino/5JUP_PROTOCOL/PIGGYBACKING/COD1_C2_1S_50PS/'
data_dir = 'COD1_C2_'
prmtop_path = '5JUP_GC_179C_wat.prmtop'

###############
# WRITE FILES #
###############

# file to submit to scheduler
outfile = open('run_cpptraj_5a_avgHbond.sh','w')
outfile.write('#!/bin/bash\n' +\
	'#BSUB -e err_avgHbond\n' +\
	'#BSUB -o out_avgHbond\n' +\
	'#BSUB -q exx96\n' +\
	'#BSUB -J "avgHbond_CPU"\n' +\
	'#BSUB -n 1\n\n' +\
	'# env\n' +\
	'export PATH=/home/apps/CENTOS7/amber/amber18/bin:$PATH\n' +\
	'export LD_LIBRARY_PATH=/home/apps/CENTOS7/amber/amber18/lib:/home/apps/CENTOS7/amber/amber18/lib64:$LD_LIBRARY_PATH\n' +\
	'export PATH=/share/apps/openmpi/1.4.4+intel-12/bin:$PATH\n' +\
	'export LD_LIBRARY_PATH=/share/apps/openmpi/1.4.4+intel-12/lib:$LD_LIBRARY_PATH\n\n' +\
	'# call cpptraj in Amber18\n' +\
	'for i in {' + str(start_expt) + '..' + str(end_expt) + '}; do\n' +\
	'	cd ' + par_dir + data_dir + '$i/DATA/\n' +\
	'	cpptraj -i cpptraj_5a_avgHbond.in\n' +\
	'done\n\n')
outfile.close()


# experimental files
for i in range(start_expt,end_expt + 1):
	outfile = open(par_dir + data_dir + str(i) + '/DATA/cpptraj_5a_avgHbond.in', 'w')
	outfile.write('# This script is to examine the average H-bonding of CAR residues.\n' +\
		'parm ' + par_dir + prmtop_path + '\n' +\
		'trajin ' + par_dir + data_dir + str(i) + '/mdcrd_nd_' + str(i) + ' ' + str(start_analysis_frame) + ' last\n\n' +\

		'### A-site anticodon nt1 to A-site codon nt1 ###\n' +\
		'hbond nhb_AVE_169_all_175_all :169|:175 avgout nhb_AVE_169_all_175_all.dat\n' +\
		'### A-site anticodon nt2 to A-site codon nt1 ###\n' +\
		'hbond nhb_AVE_168_all_175_all :168|:175 avgout nhb_AVE_168_all_175_all.dat\n\n' +\

		'### A-site anticodon nt1 to A-site codon nt2 ###\n' +\
		'hbond nhb_AVE_169_all_176_all :169|:176 avgout nhb_AVE_169_all_176_all.dat\n' +\
		'### A-site anticodon nt2 to A-site codon nt2 ###\n' +\
		'hbond nhb_AVE_168_all_176_all :168|:176 avgout nhb_AVE_168_all_176_all.dat\n' +\
		'### A-site anticodon wobble to A-site codon nt2 ###\n' +\
		'hbond nhb_AVE_167_all_176_all :167|:176 avgout nhb_AVE_167_all_176_all.dat\n\n' +\

		'### A-site anticodon nt2 to A-site codon wobble ###\n' +\
		'hbond nhb_AVE_168_all_177_all :168|:177 avgout nhb_AVE_168_all_177_all.dat\n' +\
		'### A-site anticodon wobble to A-site codon wobble ###\n' +\
		'hbond nhb_AVE_167_all_177_all :167|:177 avgout nhb_AVE_167_all_177_all.dat\n' +\
		'### C1054 to A-site codon wobble ###\n' +\
		'hbond nhb_AVE_105_all_177_all :105|:177 avgout nhb_AVE_105_all_177_all.dat\n\n' +\

		'### A-site anticodon wobble to +1 codon nt1 ###\n' +\
		'hbond nhb_AVE_167_all_178_all :167|:178 avgout nhb_AVE_167_all_178_all.dat\n' +\
		'### C1054 to +1 codon nt1 ###\n' +\
		'hbond nhb_AVE_105_all_178_all :105|:178 avgout nhb_AVE_105_all_178_all.dat\n' +\
		'### A1196 to +1 codon nt1 ###\n' +\
		'hbond nhb_AVE_114_all_178_all :114|:178 avgout nhb_AVE_114_all_178_all.dat\n\n' +\

		'### C1054 to +1 codon nt2 ###\n' +\
		'hbond nhb_AVE_105_all_179_all :105|:179 avgout nhb_AVE_105_all_179_all.dat\n' +\
		'### A1196 to +1 codon nt2 ###\n' +\
		'hbond nhb_AVE_114_all_179_all :114|:179 avgout nhb_AVE_114_all_179_all.dat\n' +\
		'### R146 to +1 codon nt2 ###\n' +\
		'hbond nhb_AVE_368_all_179_all :368|:179 avgout nhb_AVE_368_all_179_all.dat\n\n' +\

		'### A1196 to +1 codon nt3 ###\n' +\
		'hbond nhb_AVE_114_all_180_all :114|:180 avgout nhb_AVE_114_all_180_all.dat\n' +\
		'### R146 to +1 codon nt3 ###\n' +\
		'hbond nhb_AVE_368_all_180_all :368|:180 avgout nhb_AVE_368_all_180_all.dat\n\n')		

	outfile.close()