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ntBre/env.yaml

Created October 1, 2024 20:32
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Debugging minimization issue
Raw
env.yaml
name: old-openeye
channels:
- conda-forge
- openeye
dependencies:
- python
- openff-qcsubmit
- openff-toolkit
- openff-interchange
- openeye-toolkits=2022.1.1
Raw
mol.sdf
-OEChem-10012415353D
34 36 0 0 0 0 0 0 0999 V2000
7.2053 0.0077 -0.9421 H 0 0 0 0 0 0 0 0 0 0 0 0
6.2811 0.4904 -0.6268 C 0 0 0 0 0 0 0 0 0 0 0 0
5.1593 -0.2188 -0.8596 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5361 0.3544 -0.4363 S 0 0 0 0 0 0 0 0 0 0 0 0
2.6482 -1.0340 -1.0121 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2782 -1.2015 -0.9636 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9252 -2.1326 -1.3723 H 0 0 0 0 0 0 0 0 0 0 0 0
0.2861 -0.3248 -0.4544 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0552 -0.5507 -0.4389 N 0 3 0 0 0 0 0 0 0 0 0 0
-1.8599 -1.7157 -0.9265 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.5724 -1.2890 -1.6376 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.4263 -2.0531 -0.0543 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.1917 -2.9226 -1.5709 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0010 -3.6111 -1.8315 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.6718 -2.6797 -2.4999 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.5273 -3.4590 -0.8904 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.8044 0.4985 0.1329 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.1967 0.5604 0.2914 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.8484 -0.2419 -0.0320 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.7413 1.6972 0.8861 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.8173 1.7594 1.0156 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9292 2.7596 1.3193 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.3823 3.6323 1.7789 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.5455 2.7038 1.1644 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9108 3.5196 1.4961 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0034 1.5636 0.5685 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6807 1.2246 0.2506 S 0 0 0 0 0 0 0 0 0 0 0 0
3.5967 -2.3270 -1.7143 S 0 0 0 0 0 0 0 0 0 0 0 0
5.2373 -1.5568 -1.5024 C 0 0 0 0 0 0 0 0 0 0 0 0
6.2388 -2.1201 -1.8638 O 0 0 0 0 0 0 0 0 0 0 0 0
6.3895 1.8374 0.0033 C 0 0 0 0 0 0 0 0 0 0 0 0
6.8832 2.5302 -0.6886 H 0 0 0 0 0 0 0 0 0 0 0 0
7.0296 1.7792 0.8916 H 0 0 0 0 0 0 0 0 0 0 0 0
5.4266 2.2628 0.2946 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 2 0 0 0 0
2 31 1 0 0 0 0
3 4 1 0 0 0 0
3 29 1 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
5 28 1 0 0 0 0
6 7 1 0 0 0 0
6 8 1 0 0 0 0
8 9 2 0 0 0 0
8 27 1 0 0 0 0
9 10 1 0 0 0 0
9 17 1 0 0 0 0
10 11 1 0 0 0 0
10 12 1 0 0 0 0
10 13 1 0 0 0 0
13 14 1 0 0 0 0
13 15 1 0 0 0 0
13 16 1 0 0 0 0
17 18 1 0 0 0 0
17 26 2 0 0 0 0
18 19 1 0 0 0 0
18 20 2 0 0 0 0
20 21 1 0 0 0 0
20 22 1 0 0 0 0
22 23 1 0 0 0 0
22 24 2 0 0 0 0
24 25 1 0 0 0 0
24 26 1 0 0 0 0
26 27 1 0 0 0 0
28 29 1 0 0 0 0
29 30 2 0 0 0 0
31 32 1 0 0 0 0
31 33 1 0 0 0 0
31 34 1 0 0 0 0
M CHG 1 9 1
M END
> <grid_ids>
[(-165,), (-150,), (-135,), (-120,), (-105,), (-90,), (-75,), (-60,), (-45,), (-30,), (-15,), (0,), (15,), (30,), (45,), (60,), (75,), (90,), (105,), (120,), (135,), (150,), (165,), (180,)]
$$$$
Raw
try.py
from openff.interchange.drivers import get_openmm_energies
from openff.toolkit import ForceField, Molecule
from openff.units import unit
ff = ForceField("openff-2.2.0.offxml")
mol = Molecule.from_file("mol.sdf")
ic = ff.create_interchange(mol.to_topology())
orig = get_openmm_energies(ic).total_energy.m_as(unit.kilocalories_per_mole)
ic.minimize()
new = get_openmm_energies(ic).total_energy.m_as(unit.kilocalories_per_mole)
print(orig)
print(new)
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