IndexError: list index out of range

[ghost]

No description provided.

[mattwthompson]

Could you also post the files you used to generate this error? My guess without looking at the code is that dihedral_style opls is not implemented

[ctk3b]

I believe opls is actually implemented:

InterMol/intermol/lammps/lammps_parser.py

Line 175 in 8d77a4f

elif dihedral == FourierDihedral:

Hard to tell without the input file but the error suggests that the dihedral coefficients are insufficiently or incorrectly specified or that InterMol does not have support for the format in which you specified them.

[roar40]

I have encountered the same problem with opls type dihedrals. I added some print() commands to intermol/forces/forcefunctions.py.

Here is my test input for imidazole molecule:
Data file:
LAMMPS data file via write_data, version 2 Aug 2023, timestep = 0, units = real

8 atoms
8 bonds
11 angles
1 dihedrals
0 impropers

8 atom types
8 bond types
11 angle types
11 dihedral types

0 5.5 xlo xhi
0 13 ylo yhi
0 2 zlo zhi

Masses

1 14.007
2 12.011
3 14.007
4 12.011
5 12.011
6 1.008
7 1.008
8 1.008

Pair Coeffs

1 0.17 3.25
2 0.07 3.55
3 0.17 3.25
4 0.07 3.55
5 0.07 3.55
6 0.03 2.42
7 0.03 2.42
8 0.03 2.42

Bond Coeffs

1 367 1.08
2 367 1.08
3 367 1.08
4 477 1.343
5 427 1.381
6 488 1.335
7 410 1.394
8 520 1.37

Angle Coeffs

1 70 109.8
2 70 110
3 35 120
4 35 120
5 70 120
6 35 120
7 35 128.2
8 70 111
9 35 121.6
10 35 130.7
11 70 106.3

Dihedral Coeffs

1 0.0 4.65 0.0 0.0

Atoms

1 1 1 -0.257 2.3095844 3.33866316 1
2 1 2 0.275 1.51946258 2.23032123 1
3 1 6 0.078 0.4394873 2.22842121 1
4 1 3 -0.5629999999999999 2.2932654 1.16993296 1
5 1 4 0.185 3.57943166 1.55862099 1
6 1 7 0.075 4.43789688 0.90333109 1
7 1 5 -0.286 3.61532385 2.90202147 1
8 1 8 0.187 4.50017903 3.52131861 1

Velocities

1 0 0 0
2 0 0 0
3 0 0 0
4 0 0 0
5 0 0 0
6 0 0 0
7 0 0 0
8 0 0 0

Bonds

1 4 1 2
2 5 1 7
3 6 2 4
4 1 2 3
5 7 4 5
6 8 5 7
7 2 5 6
8 3 7 8

Angles

1 1 2 1 7
2 3 1 2 3
3 4 3 2 4
4 5 1 2 4
5 2 2 4 5
6 6 4 5 6
7 7 6 5 7
8 8 4 5 7
9 9 1 7 8
10 10 5 7 8
11 11 1 7 5

Dihedrals

1 1 4 2 1 7

Input file:

units real
atom_style full

dimension 3
boundary p p p

pair_style lj/cut/coul/long 11.0 11.0
pair_modify mix geometric

bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style harmonic

special_bonds lj/coul 0.0 0.0 0.5
kspace_style pppm 0.0001

read_data Imi.data

Error:

<class 'intermol.forces.harmonic_angle_type.HarmonicAngle'>
HarmonicAngle
[Unit({BaseUnit(base_dim=BaseDimension("amount"), name="mole", symbol="mol"): -1.0, BaseUnit(base_dim=BaseDimension("angle"), name="radian", symbol="rad"): -2.0, ScaledUnit(factor=4.184, master=kilojoule, name='kilocalorie', symbol='kcal'): 1.0}), Unit({BaseUnit(base_dim=BaseDimension("angle"), name="degree", symbol="deg"): 1.0})]
['k', 'theta']
['11', '70', '106.3']
{'k': Quantity(value=70.0, unit=kilocalorie/(moleradian**2))}
['11', '70', '106.3']
{'k': Quantity(value=70.0, unit=kilocalorie/(moleradian**2)), 'theta': Quantity(value=106.3, unit=degree)}
<class 'intermol.forces.fourier_dihedral_type.FourierDihedral'>
FourierDihedral
[Unit({BaseUnit(base_dim=BaseDimension("amount"), name="mole", symbol="mol"): -1.0, ScaledUnit(factor=4.184, master=kilojoule, name='kilocalorie', symbol='kcal'): 1.0}), Unit({BaseUnit(base_dim=BaseDimension("amount"), name="mole", symbol="mol"): -1.0, ScaledUnit(factor=4.184, master=kilojoule, name='kilocalorie', symbol='kcal'): 1.0}), Unit({BaseUnit(base_dim=BaseDimension("amount"), name="mole", symbol="mol"): -1.0, ScaledUnit(factor=4.184, master=kilojoule, name='kilocalorie', symbol='kcal'): 1.0}), Unit({BaseUnit(base_dim=BaseDimension("amount"), name="mole", symbol="mol"): -1.0, ScaledUnit(factor=4.184, master=kilojoule, name='kilocalorie', symbol='kcal'): 1.0}), Unit({BaseUnit(base_dim=BaseDimension("amount"), name="mole", symbol="mol"): -1.0, ScaledUnit(factor=4.184, master=kilojoule, name='kilocalorie', symbol='kcal'): 1.0})]
['c1', 'c2', 'c3', 'c4', 'c5']
['1', '0.0', '4.65', '0.0', '0.0']
{'c1': Quantity(value=0.0, unit=kilocalorie/mole)}
['1', '0.0', '4.65', '0.0', '0.0']
{'c1': Quantity(value=0.0, unit=kilocalorie/mole), 'c2': Quantity(value=4.65, unit=kilocalorie/mole)}
['1', '0.0', '4.65', '0.0', '0.0']
{'c1': Quantity(value=0.0, unit=kilocalorie/mole), 'c2': Quantity(value=4.65, unit=kilocalorie/mole), 'c3': Quantity(value=0.0, unit=kilocalorie/mole)}
['1', '0.0', '4.65', '0.0', '0.0']
{'c1': Quantity(value=0.0, unit=kilocalorie/mole), 'c2': Quantity(value=4.65, unit=kilocalorie/mole), 'c3': Quantity(value=0.0, unit=kilocalorie/mole), 'c4': Quantity(value=0.0, unit=kilocalorie/mole)}
['1', '0.0', '4.65', '0.0', '0.0']
Traceback (most recent call last):
File "/home/yr/InterMol/intermol/convert.py", line 811, in
main()
File "/home/yr/InterMol/intermol/convert.py", line 229, in main
system, prefix = _load_lammps(lammps_in=lammps_in)
File "/home/yr/InterMol/intermol/convert.py", line 605, in _load_lammps
system = lmp.load(in_file=lammps_in)
File "/home/yr/anaconda3/envs/Intermol/lib/python3.10/site-packages/intermol/lammps/lammps_parser.py", line 34, in load
return parser.read()
File "/home/yr/anaconda3/envs/Intermol/lib/python3.10/site-packages/intermol/lammps/lammps_parser.py", line 315, in read
self.read_data(self.data_file)
File "/home/yr/anaconda3/envs/Intermol/lib/python3.10/site-packages/intermol/lammps/lammps_parser.py", line 421, in read_data
parsable_keywordskeyword
File "/home/yr/anaconda3/envs/Intermol/lib/python3.10/site-packages/intermol/lammps/lammps_parser.py", line 726, in parse_dihedral_coeffs
self.parse_force_coeffs(data_lines, "Dihedral",
File "/home/yr/anaconda3/envs/Intermol/lib/python3.10/site-packages/intermol/lammps/lammps_parser.py", line 701, in parse_force_coeffs
kwds = self.create_kwds_from_entries(fields, force_class,
File "/home/yr/anaconda3/envs/Intermol/lib/python3.10/site-packages/intermol/lammps/lammps_parser.py", line 218, in create_kwds_from_entries
return ff.create_kwds_from_entries(self.unitvars, self.paramlist,
File "/home/yr/anaconda3/envs/Intermol/lib/python3.10/site-packages/intermol/forces/forcefunctions.py", line 143, in create_kwds_from_entries
kwds[p] = float(entries[offset+i]) * u[i]
IndexError: list index out of range

It seems that the program expects 5th coefficient for opls dihedral. When I change dihedral from 1 0.0 4.65 0.0 0.0 to 1 0.0 4.65 0.0 0.0 0.0 there is no error in the output:

<class 'intermol.forces.harmonic_angle_type.HarmonicAngle'>
HarmonicAngle
[Unit({BaseUnit(base_dim=BaseDimension("amount"), name="mole", symbol="mol"): -1.0, BaseUnit(base_dim=BaseDimension("angle"), name="radian", symbol="rad"): -2.0, ScaledUnit(factor=4.184, master=kilojoule, name='kilocalorie', symbol='kcal'): 1.0}), Unit({BaseUnit(base_dim=BaseDimension("angle"), name="degree", symbol="deg"): 1.0})]
['k', 'theta']
['11', '70', '106.3']
{'k': Quantity(value=70.0, unit=kilocalorie/(moleradian**2))}
['11', '70', '106.3']
{'k': Quantity(value=70.0, unit=kilocalorie/(moleradian**2)), 'theta': Quantity(value=106.3, unit=degree)}
<class 'intermol.forces.fourier_dihedral_type.FourierDihedral'>
FourierDihedral
[Unit({BaseUnit(base_dim=BaseDimension("amount"), name="mole", symbol="mol"): -1.0, ScaledUnit(factor=4.184, master=kilojoule, name='kilocalorie', symbol='kcal'): 1.0}), Unit({BaseUnit(base_dim=BaseDimension("amount"), name="mole", symbol="mol"): -1.0, ScaledUnit(factor=4.184, master=kilojoule, name='kilocalorie', symbol='kcal'): 1.0}), Unit({BaseUnit(base_dim=BaseDimension("amount"), name="mole", symbol="mol"): -1.0, ScaledUnit(factor=4.184, master=kilojoule, name='kilocalorie', symbol='kcal'): 1.0}), Unit({BaseUnit(base_dim=BaseDimension("amount"), name="mole", symbol="mol"): -1.0, ScaledUnit(factor=4.184, master=kilojoule, name='kilocalorie', symbol='kcal'): 1.0}), Unit({BaseUnit(base_dim=BaseDimension("amount"), name="mole", symbol="mol"): -1.0, ScaledUnit(factor=4.184, master=kilojoule, name='kilocalorie', symbol='kcal'): 1.0})]
['c1', 'c2', 'c3', 'c4', 'c5']
['1', '0.0', '4.65', '0.0', '0.0', '0.0']
{'c1': Quantity(value=0.0, unit=kilocalorie/mole)}
['1', '0.0', '4.65', '0.0', '0.0', '0.0']
{'c1': Quantity(value=0.0, unit=kilocalorie/mole), 'c2': Quantity(value=4.65, unit=kilocalorie/mole)}
['1', '0.0', '4.65', '0.0', '0.0', '0.0']
{'c1': Quantity(value=0.0, unit=kilocalorie/mole), 'c2': Quantity(value=4.65, unit=kilocalorie/mole), 'c3': Quantity(value=0.0, unit=kilocalorie/mole)}
['1', '0.0', '4.65', '0.0', '0.0', '0.0']
{'c1': Quantity(value=0.0, unit=kilocalorie/mole), 'c2': Quantity(value=4.65, unit=kilocalorie/mole), 'c3': Quantity(value=0.0, unit=kilocalorie/mole), 'c4': Quantity(value=0.0, unit=kilocalorie/mole)}
['1', '0.0', '4.65', '0.0', '0.0', '0.0']
{'c1': Quantity(value=0.0, unit=kilocalorie/mole), 'c2': Quantity(value=4.65, unit=kilocalorie/mole), 'c3': Quantity(value=0.0, unit=kilocalorie/mole), 'c4': Quantity(value=0.0, unit=kilocalorie/mole), 'c5': Quantity(value=0.0, unit=kilocalorie/mole)}
INFO 2024-06-19 13:08:45 Finished!

Output for dihedrals in .gro file:
[ dihedrals ]
; i j k l func
4 2 1 7 3 1.94556000e+01 -0.00000000e+00 -1.94556000e+01 -0.00000000e+00 -0.00000000e+00 -0.00000000e+00