Issues when reading charmm parameters file

[dim-99]

Hi,

I'm trying to read Charmm parameter file to construct pcbaa polymer. My code is,

`from pysimm import lmps
from pysimm import system
from pysimm import forcefield

from pysimm.apps.random_walk import random_walk, random_walk_tacticity
from pysimm.apps.random_walk import check_tacticity
from pysimm.apps.random_walk import random_walk, random_walk_tacticity, check_tacticity
import matplotlib.pyplot as mplp

s = system.System()
f = forcefield.Charmm()
m = s.molecules.add(system.Molecule())`

then I constructed molecule with,

`gaff_CG2DC3 = s.particle_types.add(f.particle_types.get('CG2DC3')[0].copy())
gaff_CG2DC1 = s.particle_types.add(f.particle_types.get('CG2DC1')[0].copy())
gaff_CG2O1 = s.particle_types.add(f.particle_types.get('CG2O1')[0].copy())
gaff_CG321 = s.particle_types.add(f.particle_types.get('CG321')[0].copy())
gaff_CG324 = s.particle_types.add(f.particle_types.get('CG324')[0].copy())
gaff_CG2O3 = s.particle_types.add(f.particle_types.get('CG2O3')[0].copy())
gaff_HGA5 = s.particle_types.add(f.particle_types.get('HGA5')[0].copy())
gaff_HGA4 = s.particle_types.add(f.particle_types.get('HGA4')[0].copy())
gaff_HGA2 = s.particle_types.add(f.particle_types.get('HGA2')[0].copy())
gaff_HGP2 = s.particle_types.add(f.particle_types.get('HGP2')[0].copy())
gaff_OG2D1 = s.particle_types.add(f.particle_types.get('OG2D1')[0].copy())
gaff_OG2D2 = s.particle_types.add(f.particle_types.get('OG2D2')[0].copy())
gaff_NG3P2 = s.particle_types.add(f.particle_types.get('NG3P2')[0].copy())

C1 = s.particles.add(system.Particle(type=gaff_CG2DC3, x=0, y=0, z=0, charge=-0.417000, molecule=m))
C2 = s.add_particle_bonded_to(system.Particle(type=gaff_CG2DC1, x=0, y=0, z=1.5419, charge=-0.097000, molecule=m), C1, f)
H3 = s.add_particle_bonded_to(system.Particle(type=gaff_HGA5, x=1.0218 , y=0, z=-0.3878, charge=0.210000, molecule=m), C1, f)
H4 = s.add_particle_bonded_to(system.Particle(type=gaff_HGA5, x=-0.4291 , y=-0.9533, z=-0.3291, charge=0.210000, molecule=m), C1, f)
C5 = s.add_particle_bonded_to(system.Particle(type=gaff_CG2O1, x=0.4192, y=1.3138 , z=2.2238, charge=0.479000, molecule=m), C2, f)
H6 = s.add_particle_bonded_to(system.Particle(type=gaff_HGA4, x=-1.0564 , y=-0.1017, z=1.8266, charge=0.150000, molecule=m), C2, f)
O7 = s.add_particle_bonded_to(system.Particle(type=gaff_OG2D1, x=-0.3907, y=1.8257, z=3.0075, charge=-0.531000, molecule=m), C5, f)
N8 = s.add_particle_bonded_to(system.Particle(type=gaff_NG2S1, x= 1.6654, y=1.8812, z=2.0153, charge=-0.32900, molecule=m), C5, f )
C9 = s.add_particle_bonded_to(system.Particle(type=gaff_CG321, x=2.6544, y=1.4433, z=1.0462, charge=-0.083000, molecule=m),N8, f )
H10 = s.add_particle_bonded_to(system.Particle(type=gaff_HGA2, x=2.6622, y=0.3620, z=0.9367, charge=0.090000, molecule=m), C9, f )
H11 = s.add_particle_bonded_to(system.Particle(type=gaff_HGA2, x=3.6519, y= 1.7467, z=1.3793, charge=0.090000, molecule=m), C9, f)
H12 = s.add_particle_bonded_to(system.Particle(type=gaff_HGP1, x=2.1280, y=1.7515, z=2.8923, charge=0.274000, molecule=m), N8, f)
C13 = s.add_particle_bonded_to(system.Particle(type=gaff_CG321, x=2.3494, y=2.1061, z=-0.3100 charge=-0.153000, molecule=m), C9, f)
H14 = s.add_particle_bonded_to(system.Particle(type=gaff_HGA2, x=2.3839, y=1.3676, z=-1.0836, charge=0.090000, molecule=m), C13, f)
H15 = s.add_particle_bonded_to(system.Particle(type=gaff_HGA2, x=1.3747, y=2.5465, z=-0.2806, charge=0.090000, molecule=m), C13, f)
C16 = s.add_particle_bonded_to(system.Particle(type=gaff_CG324, x=3.3975, y=3.1976, z=-0.5953 charge=0.129000, molecule=m),C16, f)
H17 = s.add_particle_bonded_to(system.Particle(type=gaff_HGA2, x=4.3790, y=2.7784, z=-0.5187, charge=0.090000, molecule=m), C16, f)
H18 = s.add_particle_bonded_to(system.Particle(type=gaff_HGA2, x=3.2912, y=3.9890, z=0.1170, charge=0.090000, molecule=m), C16, f)
N19 = s.add_particle_bonded_to(system.Particle(type=gaff_NG3P2, x=3.1958, y=3.7283, z=-1.9512, charge=-0.3910000, molecule=m),C16,f)
H20 = s.add_particle_bonded_to(system.Particle(type=gaff_HGP2, x=3.9652, y=3.4612, z=-2.5315, charge=0.320000, molecule=m),N19,f )
H21 = s.padd_particle_bonded_to(system.Particle(type=gaff_HGP2, x=2.3476, y=3.3589, z=-2.3310, charge=0.320000, molecule=m),N19,f)
C22 = s.add_particle_bonded_to(system.Particle(type=gaff_CG324, x=3.1101, y=5.1948, z=-1.8957 charge=0.173000, molecule=m),N19,f)
H23 = s.add_particle_bonded_to(system.Particle(type=gaff_HGA2, x=3.9215, y=5.5777, z=-1.3127, charge=0.090000, molecule=m),C22,f)
H24 = s.add_particle_bonded_to(system.Particle(type=gaff_HGA2, x=2.1820, y=5.4811, z=-1.4467 charge=0.090000, molecule=m),C22,f)
C25 = s.add_particle_bonded_to(system.Particle(type=gaff_CG321, x=3.1881, y=5.7679, z=-3.3230 charge=-0.242000, molecule=m),C22,f)
H26 = s.add_particle_bonded_to(system.Particle(type=gaff_HGA2, x=4.1187, y=5.4867, z=-3.7699 charge=0.090000, molecule=m),C25,f)
H27 = s.add_particle_bonded_to(system.Particle(type=gaff_HGA2, x=2.3801, y=5.3804, z=-3.9076 charge=0.090000, molecule=m),C25,f)
C28 = s.add_particle_bonded_to(system.Particle(type=gaff_CG2O3 , x=3.0898, y=7.3037, z=-3.2655, charge=0.598000, molecule=m),C25,f)
O29 = s.add_particle_bonded_to(system.Particle(type=gaff_OG2D2, x=2.7764, y=7.9519, z=-2.0299, charge=-0.760000, molecule=m),C28,f)
O30 = s.add_particle_bonded_to(system.Particle(type=gaff_OG2D2, x=3.2842, y=7.9902, z=-4.3021, charge=-0.760000, molecule=m),C28,f)

`
with that I tried,

`s.apply_forcefield(f, charges='none')
lnkr_atoms = {'head': 1, 'tail': 2}

for itm, nm in lnkr_atoms.items():
s.particles[nm].linker = itm

p = forcefield.Charmm()
p.parse_add_file('pcbaa.prm')`

It gave me the error,

KeyError Traceback (most recent call last)
/scratch/local/44140053/ipykernel_189726/397443237.py in
1 p = forcefield.Charmm()
----> 2 p.parse_add_file('pcbaa.prm')

/orange/colina/dkodituwakku/peggox/pysimm/pysimm/forcefield/charmm.py in parse_add_file(self, file)
590 tmp = getattr(self, 'nbfix_types')._dict
591 for t in tmp.keys():
--> 592 outp_obj['nbfix_types'].append(tmp[t].dict)
593
594 DATA_PATH = os.path.join(os.path.dirname(os.path.realpath(file)), os.pardir, 'data', 'forcefields', 'charmm')

KeyError: 'nbfix_types'

Could you let me know what I'm doing wrong?

Thank you