Homec4science
Diffusion lammps (lammps-icms) Browse

lammps/tools/moltemplate/common/amber/amberparm_improper_to_lt.py
16eed7a05366lammps-icms

Last Change
Raw File

amberparm_improper_to_lt.py
View Options

#!/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
#sys.stdout.write(' '+impropertype+' @atom:'+at1+' @atom:'+at2+' @atom:'+at3+' @atom:'+at4+'\n')
# Oops. This is incorrect.
# In moltemplate, the central atom is the first atom,
# In "gaff.dat", the central atom is the third atom
# http://archive.ambermd.org/201307/0519.html
#impropertype = '@improper:'+atype3+'-'+atype1+'-'+atype2+'-'+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 (gaff_imp.py)") {\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')
# The improper-angle is the angle between the planes
# defined by at1,at2,at3, and at2,at3,at3
# and we list the atoms in this order.
# NOTE: In "gaff.dat", the central atom is the third atom (at3)
# so we have to take this into account when matching atom order.
# http://archive.ambermd.org/201307/0519.html
sys.stdout.write(' } # (end of Impropers By Type)\n')
sys.stdout.write('\n')
# NOTE: AMBER documentation is not clear how the improper angle is defined.
# It's not clear if we should be using the dihedral angle between
# planes I-J-K and J-K-L. As of 2014-4, improper_style cvff does this.
# Even if we create improper interactions with the angle defined between
# the wrong planes, at least the minima should be the same
# (0 degrees or 180 degrees).
# So I'm not too worried we are getting this detail wrong long as
# we generate new impropers realizing that the 3rd atom (K) is the
# central atom (according to AMBER conventions).
#
# http://structbio.vanderbilt.edu/archives/amber-archive/2007/0408.php
#
# Currently, we only apply improper torsional angles for atoms
# in a planar conformations. Is it clear?
# Junmei
c4science · Help