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lammps/tools/moltemplate/common/amber/amberparm_pair_to_lt.py
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amberparm_pair_to_lt.py
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#!/usr/bin/env python
import sys
lines_gaff = sys.stdin.readlines()
#pair_style = 'lj/charmm/coul/long'
# NOTE: Long-range coulombic forces were disabled intentionally. (See below)
# If you want to use long-range electrostatics, uncomment these lines:
# Instead I use hybrid lj/charmm/coul/charmm by default, because
# LAMMPS complains if you attempt to use lj/charmm/coul/long on a
# system if it does not contain any charged particles.
# Currently, moltemplate does not assign atomic charge,
# so this problem occurs frequently.
#pair_style = 'lj/charmm/coul/charmm'
pair_style = 'lj/charmm/coul/long'
sys.stdout.write(' write_once(\"In Settings\") {\n')
for i in range(0, len(lines_gaff)):
line = lines_gaff[i]
tokens= line.split()
atype = tokens[0]
# UGGHHH
# OLD CODE:
#sig=tokens[1]
# CORRECTION #1
# It looks the number in this part of the file is an atom radii, not a
# diameter. In other words, this number is 0.5*sigma instead of sigma.
# So we multiply it by 2.0.
#sig=str(2.0*float(tokens[1]))
#
# CORRECTION #2
# It also appears as though they are using this convention for LennardJones
# U(r)=epsilon*((s/r)^12-2*(s/r)^6) instead of 4*eps*((s/r)^12-(s/r)^6)
# ...where "s" is shorthand for "sigma"..
# This means we must ALSO multiply sigma in gaff.dat by 2**(-1.0/6)
# (This change makes the two U(r) formulas equivalent.)
# I had to figure this out by iterations of trial and error.
# The official AMBER documentation is quite vague about the LJ parameters.
# My apologies to everyone effected by this bug! -Andrew 2014-5-19
# http://ambermd.org/formats.html#parm.dat
# http://structbio.vanderbilt.edu/archives/amber-archive/2009/5072.php)
sig=str(float(tokens[1])*2.0*pow(2.0, (-1.0/6.0)))
eps=tokens[2]
comments=' '.join(tokens[3:])
sys.stdout.write(' pair_coeff @atom:'+atype+' @atom:'+atype+' '+pair_style+' '+eps+' '+sig+' # '+comments+'\n')
sys.stdout.write(' } # (end of pair_coeffs)\n')
sys.stdout.write('\n')
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