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lammps/tools/moltemplate/common/amber/amberparm_improper_to_lt.py
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amberparm_improper_to_lt.py
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#!/usr/bin/env python
import sys
lines_gaff = sys.stdin.readlines()
improper_style_name = 'cvff'
sys.stdout.write(' write_once("In Settings") {\n')
for i in range(0, len(lines_gaff)):
line = lines_gaff[i]
atypes = line[:11].split('-')
atype1 = atypes[0].strip()
atype2 = atypes[1].strip()
atype3 = atypes[2].strip()
atype4 = atypes[3].strip()
at1 = atype1.replace('X','*')
at2 = atype2.replace('X','*')
at3 = atype3.replace('X','*')
at4 = atype4.replace('X','*')
impropertype = '@improper:'+atype1+'-'+atype2+'-'+atype3+'-'+atype4
tokens= line[11:].split()
Kn = float(tokens[0])
dn = float(tokens[1])
n = int(float(tokens[2]))
comments=' '.join(tokens[3:])
if (dn < 0.001):
sys.stdout.write(' improper_coeff '+impropertype+' '+improper_style_name+' '+str(Kn)+' 1 '+str(n)+' # '+comments+'\n')
elif (179.999 < abs(dn) < 180.001):
sys.stdout.write(' improper_coeff '+impropertype+' '+improper_style_name+' '+str(Kn)+' -1 '+str(n)+' # '+comments+'\n')
else:
sys.stderr.write('Error: Illegal bondImproper parameters:\n'
' As of 2013-8-03, LAMMPS doens hot have an improper style\n'
' which can handle impropers with gamma != 0 or 180\n')
exit(-1)
sys.stdout.write(' } # (end of improper_coeffs)\n')
sys.stdout.write('\n')
sys.stdout.write(' write_once("Data Impropers By Type") {\n')
for i in range(0, len(lines_gaff)):
line = lines_gaff[i]
atypes = line[:11].split('-')
atype1 = atypes[0].strip()
atype2 = atypes[1].strip()
atype3 = atypes[2].strip()
atype4 = atypes[3].strip()
at1 = atype1.replace('X','*')
at2 = atype2.replace('X','*')
at3 = atype3.replace('X','*')
at4 = atype4.replace('X','*')
impropertype = '@improper:'+atype1+'-'+atype2+'-'+atype3+'-'+atype4
sys.stdout.write(' '+impropertype+' @atom:'+at1+' @atom:'+at2+' @atom:'+at3+' @atom:'+at4+'\n')
sys.stdout.write(' } # (end of Impropers By Type)\n')
sys.stdout.write('\n')
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