openmm
AmberTools 23 causes openmmforcefield tests to fail
The update from ambertools 22 to 23 appears to cause the tests to fail:
____________________________________________________________________________________________________________________ TestSystemGenerator.test_add_molecules _____________________________________________________________________________________________________________________
self = <openmmforcefields.tests.test_system_generator.TestSystemGenerator testMethod=test_add_molecules>
def test_add_molecules(self):
"""Test that Molecules can be added to SystemGenerator later"""
for small_molecule_forcefield in SMALL_MOLECULE_FORCEFIELDS:
print(small_molecule_forcefield)
# Create a SystemGenerator for this force field
generator = SystemGenerator(forcefields=self.amber_forcefields,
small_molecule_forcefield=small_molecule_forcefield)
# Add molecules for each test system separately
for name, testsystem in self.testsystems.items():
molecules = testsystem['molecules']
# Add molecules
generator.add_molecules(molecules)
# Parameterize molecules
for molecule in molecules:
# DEBUG
if not (small_molecule_forcefield == 'gaff-2.11'):
continue
openmm_topology = molecule.to_topology().to_openmm()
with Timer() as t1:
try:
print(f'{small_molecule_forcefield} {name} {molecule.name} first generation')
system = generator.create_system(openmm_topology)
except ValueError as e:
> raise(e)
tests/test_system_generator.py:341:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_system_generator.py:339: in test_add_molecules
system = generator.create_system(openmm_topology)
generators/system_generators.py:332: in create_system
system = self.forcefield.createSystem(topology, **forcefield_kwargs)
../../../../micromamba/envs/openmmforcefields/lib/python3.10/site-packages/openmm/app/forcefield.py:1218: in createSystem
templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds)
../../../../micromamba/envs/openmmforcefields/lib/python3.10/site-packages/openmm/app/forcefield.py:1423: in _matchAllResiduesToTemplates
if generator(self, res):
generators/template_generators.py:552: in generator
return super().generator(forcefield, residue)
generators/template_generators.py:325: in generator
forcefield.loadFile(StringIO(ffxml_contents))
../../../../micromamba/envs/openmmforcefields/lib/python3.10/site-packages/openmm/app/forcefield.py:288: in loadFile
self.registerAtomType(type.attrib)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <openmm.app.forcefield.ForceField object at 0x17cc889a0>, parameters = {'class': 'c5', 'element': 'C', 'mass': '12.01', 'name': 'c5'}
def registerAtomType(self, parameters):
"""Register a new atom type."""
name = parameters['name']
if name in self._atomTypes:
> raise ValueError('Found multiple definitions for atom type: '+name)
E ValueError: Found multiple definitions for atom type: c5
../../../../micromamba/envs/openmmforcefields/lib/python3.10/site-packages/openmm/app/forcefield.py:437: ValueError
This appears to be due to a new gaff2.dat that is distributed with this release (and possibly earlier?) that includes new types:
AMBER General Force Field for organic molecules (Version 2.2.20, March 2021)
The parmchk2 tool now generates parameters for this version, it appears.
For example, for the bace testsystem CAT-13d ligand with gaff-2.11, ambertools=22 generates the frcmod file:
Remark line goes here
MASS
BOND
cz-n 330.20 1.399 same as c2- n, penalty score= 3.2
cz-nv 414.20 1.339 same as cz-nh, penalty score= 0.0
cz-nu 414.20 1.339 same as cz-nh, penalty score= 0.0
hn-nv 529.50 1.012 same as hn-nh, penalty score= 0.0
c3-nu 261.80 1.464 same as c3-nh, penalty score= 0.0
hn-nu 529.50 1.012 same as hn-nh, penalty score= 0.0
ANGLE
c3-n -cz 65.000 120.100 same as c2-n -c3, penalty score= 2.2
n -cz-nv 112.600 120.140 same as nh-cz-nh, penalty score= 1.8
n -cz-nu 112.600 120.140 same as nh-cz-nh, penalty score= 1.8
c -n -cz 66.400 122.150 same as c -n -c2, penalty score= 2.2
cz-nv-hn 49.200 121.150 same as cz-nh-hn, penalty score= 0.0
c3-nu-cz 64.700 125.460 same as c3-nh-cz, penalty score= 0.0
cz-nu-hn 49.200 121.150 same as cz-nh-hn, penalty score= 0.0
nu-cz-nv 112.600 120.140 same as nh-cz-nh, penalty score= 0.0
ca-c3-nu 83.900 111.390 same as ca-c3-nh, penalty score= 0.0
cx-c3-nu 86.600 103.860 same as cx-c3-nh, penalty score= 0.0
c -c3-nu 84.400 109.350 same as c -c3-nh, penalty score= 0.0
c3-nu-hn 46.400 115.990 same as c3-nh-hn, penalty score= 0.0
hn-nv-hn 39.500 115.120 same as hn-nh-hn, penalty score= 0.0
DIHE
nv-cz-n -c3 4 2.600 180.000 2.000 same as X -c2-n -X , penalty score=462.5
nu-cz-n -c3 4 2.600 180.000 2.000 same as X -c2-n -X , penalty score=462.5
n -cz-nv-hn 4 2.700 180.000 2.000 same as X -c2-nh-X , penalty score=462.5
n -cz-nu-c3 4 2.700 180.000 2.000 same as X -c2-nh-X , penalty score=462.5
n -cz-nu-hn 4 2.700 180.000 2.000 same as X -c2-nh-X , penalty score=462.5
ca-c3-nu-cz 6 0.000 0.000 2.000 same as X -c3-nh-X , penalty score= 0.0
cx-c3-nu-cz 6 0.000 0.000 2.000 same as X -c3-nh-X , penalty score= 0.0
c -c3-nu-cz 6 0.000 0.000 2.000 same as X -c3-nh-X , penalty score= 0.0
nv-cz-nu-c3 4 2.700 180.000 2.000 same as X -c2-nh-X , penalty score=462.5
nv-cz-nu-hn 4 2.700 180.000 2.000 same as X -c2-nh-X , penalty score=462.5
nu-cz-nv-hn 4 2.700 180.000 2.000 same as X -c2-nh-X , penalty score=462.5
nu-c3-cx-cx 1 0.210 0.000 3.000 same as nh-c3-c3-c3, penalty score=179.0
nu-c3-cx-hc 9 1.400 0.000 3.000 same as X -c3-c3-X , penalty score= 92.0
ca-c3-cx-cx 9 1.400 0.000 3.000 same as X -c3-c3-X , penalty score= 92.0
ca-c3-cx-hc 9 1.400 0.000 3.000 same as X -c3-c3-X , penalty score= 92.0
nv-cz-n -c 4 2.600 180.000 2.000 same as X -c2-n -X , penalty score=462.5
nu-cz-n -c 4 2.600 180.000 2.000 same as X -c2-n -X , penalty score=462.5
c -c3-cx-cx 1 0.100 0.000 3.000 same as c -c3-c3-c3, penalty score=179.0
c -c3-cx-hc 9 1.400 0.000 3.000 same as X -c3-c3-X , penalty score= 92.0
ca-c3-nu-hn 6 0.000 0.000 2.000 same as X -c3-nh-X , penalty score= 0.0
cx-c3-nu-hn 6 0.000 0.000 2.000 same as X -c3-nh-X , penalty score= 0.0
c -c3-nu-hn 6 0.000 0.000 2.000 same as X -c3-nh-X , penalty score= 0.0
IMPROPER
c -c3-n -cz 1.1 180.0 2.0 Using the default value
n -nu-cz-nv 1.1 180.0 2.0 Using the default value
cz-hn-nv-hn 1.1 180.0 2.0 Using the default value
c3-cz-nu-hn 1.1 180.0 2.0 Using the default value
ca-ca-ca-ha 1.1 180.0 2.0 Using general improper torsional angle X- X-ca-ha, penalty score= 6.0)
ca-cp-ca-ha 1.1 180.0 2.0 Using general improper torsional angle X- X-ca-ha, penalty score= 6.0)
ca-ca-cp-cp 1.1 180.0 2.0 Using the default value
c3-n -c -o 10.5 180.0 2.0 Using general improper torsional angle X- X- c- o, penalty score= 6.0)
NONBON
Now, with ambertools=23, the frcmod file is different:
Remark line goes here
MASS
c5 12.010 0.878 same as c3
BOND
cz-n 330.20 1.399 same as c2- n, penalty score= 3.2
cz-nv 414.20 1.339 same as cz-nh, penalty score= 0.0
cz-nu 414.20 1.339 same as cz-nh, penalty score= 0.0
hn-nv 529.50 1.012 same as hn-nh, penalty score= 0.0
c5-nu 261.80 1.464 same as c3-nh, penalty score= 0.0
hn-nu 529.50 1.012 same as hn-nh, penalty score= 0.0
c5-ca 250.30 1.516 same as c3-ca, penalty score= 0.0
c5-cx 244.90 1.522 same as c3-cx, penalty score= 0.0
c -c5 243.20 1.524 same as c-c3, penalty score= 0.0
ANGLE
c3-n -cz 65.000 120.100 same as c2-n -c3, penalty score= 2.2
n -cz-nv 112.600 120.140 same as nh-cz-nh, penalty score= 1.8
n -cz-nu 112.600 120.140 same as nh-cz-nh, penalty score= 1.8
c5-c -n 84.300 115.180 same as c3-c -n , penalty score= 0.0
c -n -cz 66.400 122.150 same as c -n -c2, penalty score= 2.2
cz-nv-hn 49.200 121.150 same as cz-nh-hn, penalty score= 0.0
c5-nu-cz 64.700 125.460 same as c3-nh-cz, penalty score= 0.0
cz-nu-hn 49.200 121.150 same as cz-nh-hn, penalty score= 0.0
nu-cz-nv 112.600 120.140 same as nh-cz-nh, penalty score= 0.0
ca-c5-nu 83.900 111.390 same as ca-c3-nh, penalty score= 0.0
cx-c5-nu 86.600 103.860 same as cx-c3-nh, penalty score= 0.0
c -c5-nu 84.400 109.350 same as c -c3-nh, penalty score= 0.0
c5-nu-hn 46.400 115.990 same as c3-nh-hn, penalty score= 0.0
c5-ca-ca 65.600 120.770 same as c3-ca-ca, penalty score= 0.0
c5-cx-cx 63.400 120.110 same as c3-cx-cx, penalty score= 0.0
c5-cx-hc 46.300 114.480 same as c3-cx-hc, penalty score= 0.0
c5-c -o 84.600 123.200 same as c3-c -o , penalty score= 0.0
ca-c5-cx 65.400 112.620 same as ca-c3-cx, penalty score= 0.0
c -c5-ca 65.800 111.010 same as c -c3-ca, penalty score= 0.0
c -c5-cx 65.600 111.160 same as c -c3-cx, penalty score= 0.0
hn-nv-hn 39.500 115.120 same as hn-nh-hn, penalty score= 0.0
DIHE
nv-cz-n -c3 4 2.600 180.000 2.000 same as X -c2-n -X , penalty score=462.5
nu-cz-n -c3 4 2.600 180.000 2.000 same as X -c2-n -X , penalty score=462.5
c5-c -n -c3 1 0.260 180.000 -2.000 same as c3-n -c -c3
c5-c -n -c3 1 0.500 0.000 1.000 same as c3-n -c -c3, penalty score= 0.0
n -cz-nv-hn 4 2.700 180.000 2.000 same as X -c2-nh-X , penalty score=462.5
n -cz-nu-c5 4 2.700 180.000 2.000 same as X -c2-nh-X , penalty score=462.5
n -cz-nu-hn 4 2.700 180.000 2.000 same as X -c2-nh-X , penalty score=462.5
ca-c5-nu-cz 6 0.000 0.000 2.000 same as X -c3-nh-X , penalty score= 0.0
cx-c5-nu-cz 6 0.000 0.000 2.000 same as X -c3-nh-X , penalty score= 0.0
c -c5-nu-cz 6 0.000 0.000 2.000 same as X -c3-nh-X , penalty score= 0.0
nv-cz-nu-c5 4 2.700 180.000 2.000 same as X -c2-nh-X , penalty score=462.5
nv-cz-nu-hn 4 2.700 180.000 2.000 same as X -c2-nh-X , penalty score=462.5
nu-cz-nv-hn 4 2.700 180.000 2.000 same as X -c2-nh-X , penalty score=462.5
nu-c5-ca-ca 6 0.000 0.000 2.000 same as X -c3-ca-X , penalty score= 0.0
nu-c5-cx-cx 1 0.210 0.000 3.000 same as nh-c3-c3-c3, penalty score=179.0
nu-c5-cx-hc 9 1.400 0.000 3.000 same as X -c3-c3-X , penalty score= 92.0
n -c -c5-nu 6 0.000 180.000 2.000 same as X -c -c3-X , penalty score= 0.0
o -c -c5-nu 6 0.000 180.000 2.000 same as X -c -c3-X , penalty score= 0.0
ca-c5-cx-cx 9 1.400 0.000 3.000 same as X -c3-c3-X , penalty score= 92.0
ca-c5-cx-hc 9 1.400 0.000 3.000 same as X -c3-c3-X , penalty score= 92.0
n -c -c5-ca 6 0.000 180.000 2.000 same as X -c -c3-X , penalty score= 0.0
o -c -c5-ca 6 0.000 180.000 2.000 same as X -c -c3-X , penalty score= 0.0
cx-c5-ca-ca 6 0.000 0.000 2.000 same as X -c3-ca-X , penalty score= 0.0
n -c -c5-cx 6 0.000 180.000 2.000 same as X -c -c3-X , penalty score= 0.0
o -c -c5-cx 6 0.000 180.000 2.000 same as X -c -c3-X , penalty score= 0.0
nv-cz-n -c 4 2.600 180.000 2.000 same as X -c2-n -X , penalty score=462.5
nu-cz-n -c 4 2.600 180.000 2.000 same as X -c2-n -X , penalty score=462.5
c -c5-ca-ca 6 0.000 0.000 2.000 same as X -c3-ca-X , penalty score= 0.0
c -c5-cx-cx 1 0.100 0.000 3.000 same as c -c3-c3-c3, penalty score=179.0
c -c5-cx-hc 9 1.400 0.000 3.000 same as X -c3-c3-X , penalty score= 92.0
ca-c5-nu-hn 6 0.000 0.000 2.000 same as X -c3-nh-X , penalty score= 0.0
cx-c5-nu-hn 6 0.000 0.000 2.000 same as X -c3-nh-X , penalty score= 0.0
c -c5-nu-hn 6 0.000 0.000 2.000 same as X -c3-nh-X , penalty score= 0.0
IMPROPER
c -c3-n -cz 1.1 180.0 2.0 Using the default value
n -nu-cz-nv 1.1 180.0 2.0 Using the default value
cz-hn-nv-hn 1.1 180.0 2.0 Using the default value
c5-cz-nu-hn 1.1 180.0 2.0 Using the default value
c5-ca-ca-ca 1.1 180.0 2.0 Using the default value
ca-ca-ca-ha 1.1 180.0 2.0 Using general improper torsional angle X- X-ca-ha, penalty score= 6.0)
ca-cp-ca-ha 1.1 180.0 2.0 Using general improper torsional angle X- X-ca-ha, penalty score= 6.0)
ca-ca-cp-cp 1.1 180.0 2.0 Using the default value
c5-n -c -o 10.5 180.0 2.0 Using general improper torsional angle X- X- c- o, penalty score= 6.0)
NONBON
c5 1.9069 0.1078 same as c3
It appears that the second time a molecule generates the c5 parameter, OpenMM ForceField complains that we are trying to load in a new c5 type.
There are a few problems to be solved here:
- We need to make sure
parmchk*generates parameters for the desiredgaff.dat, not just the latestgaff.dat - We need a way to enable multiple molecules whose
frcmodfiles generate new atom types to be loaded (as long as those atom types are identical)
Issue 1 is especially puzzling since we feed parmchk2 the same GAFF parameter file we are using via the-p gaff.dat argument. I suspect the code for parmchk2 has changed.
@peastman : Is there a way we could permit openmm.app.ForceField.registerAtomType() to allow multiple registrations of the same atom type provided the definitions are identical?
The alternative would require substantial editing of the ParmEd data structures, or even worse, the ffxml files, to de-duplicate entries based on what has already been registered.
Another possibility would be to completely change the way we handle GAFF and use LEaP to generate an OpenMM System, and then use convert_system_to_ffxml so that each molecule receives a completely distinct set of atom types, rather than sharing the common gaff*.xml atom types. This would be a major change in behavior that we'd have to test extensively, but in case prmchk2 ever generates conflicting new types in the frcmod file it generates for different molecules loaded into the same ForceField object, this might be the most future-proof approach.
That seems reasonable. We just need to verify that the class, element, and mass are all identical.
With https://github.com/openmm/openmm/pull/4531 patched into my local setup, I have this package's tests passing (so far) with AmberTools 23 installed
I don't know a good way to run this package's tests here against development builds of OpenMM - I patched $CONDA_PREFIX/lib/python3.11/site-packages/openmm/app/forcefield.py and refuse to let that propagate out past my machine
Is that PR finished? I've been ignoring it since you have it marked as a draft. Once it's ready we can merge it and get it into the next release.
Actually, I see it's a brand new PR. I was just confused. :) Let me know when it's ready for review.
I think it's ready as-is - I marked it as a draft only because I wasn't sure if I was going to break CI or not.
The CI runs (in the main repo) are coming in green so far, so I'd be happy to take feedback there (or here) on what to do next (add tests? test here? etc.)
As of #368, GAFF 2.2.20 from AmberTools 24.8 is working, so it looks like this can be closed. Feel free to reopen if there was something outstanding here.
