openforcefield
Bad optimized geometry for sulfonic and phosphonic acids
A Drugbank molecule with sulfonic and phosphonic acids optimizes with smirnoff99Frosst to bad geometries: valence angles O-P,S-O too large or small, S-O-H angle too small, and 1-4 distance O=S-O-H too small
To reproduce the behavior, just read in and optimize the first conformer of the accompanying DB2592_minIssue.mol2; What I get is the seconf conformer of the same molecule. Importantly, the first conformer is the MMFF94 optimized geometry to show that a) the starting geometry is reasonable and b) MMFF94 doesn't have the same pathologies. Also important is that the molecule is charged (single-conformer AM1-BCC) and I used these charges in the smirnoff optimization. The charge on the offending H is larger than I like, consistent with AM1-BCC on a strongly internally H-bonded moiety, which is why I would prefer ELF10 charging but what is there is a reasonable expectation for a use case. The resulting optimized coords seem pathological, suggestive of angle force constants that are substantially too small. Is it the smirnoff force constants to blame or is there a bug in applying them?
If the problem involves a specific molecule or file, please upload that as well.
Output DB2592_minIssue.mol2.gz
Computing environment OSX 10.14 using the Reference Platform (ie CPU) in OpenMM
Output of running conda list:
packages in environment at /Users/bayly/miniconda/envs/off_2019jun27:
ambermini 16.16.0 7 omnia
appnope 0.1.0 py36_1000 conda-forge
attrs 19.1.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
bleach 3.1.0 py_0 conda-forge
boost 1.70.0 py36haf112f3_1 conda-forge
boost-cpp 1.70.0 hd59e818_0 conda-forge
bson 0.5.8 py_0 conda-forge
bzip2 1.0.6 h1de35cc_1002 conda-forge
ca-certificates 2019.6.16 hecc5488_0 conda-forge
cairo 1.16.0 h0ab9d94_1001 conda-forge
certifi 2019.6.16 py36_0 conda-forge
cycler 0.10.0 py_1 conda-forge
dbus 1.13.6 h2f22bb5_0 conda-forge
decorator 4.4.0 py_0 conda-forge
defusedxml 0.5.0 py_1 conda-forge
entrypoints 0.3 py36_1000 conda-forge
expat 2.2.5 h6de7cb9_1003 conda-forge
fftw3f 3.3.4 2 omnia
fontconfig 2.13.1 h1027ab8_1000 conda-forge
freetype 2.10.0 h24853df_0 conda-forge
gettext 0.19.8.1 h46ab8bc_1002 conda-forge
glib 2.58.3 h9d45998_1001 conda-forge
icu 58.2 h0a44026_1000 conda-forge
ipykernel 5.1.1 py36h24bf2e0_0 conda-forge
ipython 7.5.0 py36h24bf2e0_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.4.2 py_0 conda-forge
jedi 0.14.0 py36_0 conda-forge
jinja2 2.10.1 py_0 conda-forge
jpeg 9c h1de35cc_1001 conda-forge
jsonschema 3.0.1 py36_0 conda-forge
jupyter 1.0.0 py_2 conda-forge
jupyter_client 5.2.4 py_3 conda-forge
jupyter_console 6.0.0 py_0 conda-forge
jupyter_core 4.4.0 py_0 conda-forge
kiwisolver 1.1.0 py36h770b8ee_0 conda-forge
libblas 3.8.0 10_openblas conda-forge
libcblas 3.8.0 10_openblas conda-forge
libcxx 8.0.0 3 conda-forge
libcxxabi 8.0.0 3 conda-forge
libffi 3.2.1 h6de7cb9_1006 conda-forge
libgcc 4.8.5 hdbeacc1_10 conda-forge
libgfortran 3.0.1 0 conda-forge
libiconv 1.15 h01d97ff_1005 conda-forge
liblapack 3.8.0 10_openblas conda-forge
libopenblas 0.3.6 hd44dcd8_3 conda-forge
libpng 1.6.37 h2573ce8_0 conda-forge
libsodium 1.0.16 h1de35cc_1001 conda-forge
libtiff 4.0.10 hd08fb8f_1003 conda-forge
libxml2 2.9.9 hd80cff7_0 conda-forge
lz4-c 1.8.3 h6de7cb9_1001 conda-forge
markupsafe 1.1.1 py36h1de35cc_0 conda-forge
matplotlib 3.1.0 py36_1 conda-forge
matplotlib-base 3.1.0 py36h3a684a6_1 conda-forge
mistune 0.8.4 py36h1de35cc_1000 conda-forge
msgpack-python 0.6.1 py36h04f5b5a_0 conda-forge
nbconvert 5.5.0 py_0 conda-forge
nbformat 4.4.0 py_1 conda-forge
ncurses 6.1 h0a44026_1002 conda-forge
networkx 2.3 py_0 conda-forge
notebook 5.7.8 py36_1 conda-forge
numpy 1.16.4 py36h6b0580a_0 conda-forge
olefile 0.46 py_0 conda-forge
openblas 0.3.6 hd44dcd8_3 conda-forge
OpenEye-toolkits 2019.4.2
Using smirnoff99Frosst-1.0.9.offxml for this case. Found out that the valence angle parameters assigned for the O-S-O valence angle is:
<Angle smirks="[*:1]~[#16X4:2]~[*:3]" angle="109.5" id="a30" k="140.0"/>
which has the right equilibrium angle.
Likewise the O-P-O angles have valence angle parameter:
<Angle smirks="[*:1]~[#15:2]~[*:3]" angle="109.5" id="a38" k="140.0"/>
which has the right equilib angle.
For the S-O-H:
<Angle smirks="[*:1]-[#8:2]-[*:3]" angle="113." id="a27" k="100.0"/>
which seems perhaps a little large, but the opt angle is way too small ( 81.5 degrees)
OK, so for the record (cross-posting from Slack) this is a phosphonic acid with a proton and a sulfonic acid with a proton, and the proton ends up way too close to the other oxygen coming off of the connected [sulfur/phosphorous]. Probably the angle is not stiff enough.
I've actually seen this before with a protonated phosphonic acid with GAFF, and my recollection is that we brought it up with Dave Case and he'd seen it before too. So we think this is a general issue with AMBER-type FFs for these systems and not a SMIRNOFF-specific one.
We need to: a) Make sure we have some molecule(s) presenting these parameters present in the pipeline for fitting, then b) specifically check the geometries of these after fitting to see if they're going to need a custom/special angle parameter.
Thanks for the thorough report, @cbayly13 .
I've reproduced this bug on my side. Simulating this molecule at 300K at 2fs step in OpenMM leads to a crash after a few hundred steps.
The charges on some atoms here are large [1]. I could see this accumulation of charge leading to coulomb interactions that compete with valence parameters. As you said, these charges came from a vanilla workflow, so we probably want to be able to handle this. I agree with @davidlmobley that we want to bring these conformers into the training set.
I'm including the XML system here [2], for the curious.
[1]: first conformer from the attached mol2 file
Summary
@<TRIPOS>MOLECULE
DrugBank_2592
46 48 0 0 0
SMALL
USER_CHARGES
@<TRIPOS>ATOM
1 C1 2.1618 -1.4754 2.9984 C.ar 1 <0> 0.6913
2 C2 -1.5292 0.8508 3.1538 C.2 1 <0> 0.5392
3 C3 -0.3131 -0.8110 3.7330 C.ar 1 <0> -0.2243
4 C4 0.4465 -0.0826 2.8325 C.ar 1 <0> 0.5809
5 C5 0.2801 -1.9658 4.2686 C.ar 1 <0> 0.7636
6 C6 0.1166 2.6930 -0.7029 C.3 1 <0> 0.1716
7 C7 0.4714 1.5084 0.1748 C.3 1 <0> 0.0739
8 C8 -1.2058 3.1304 -0.0805 C.3 1 <0> 0.1300
9 C9 0.0422 2.0256 1.5546 C.3 1 <0> 0.4089
10 C10 -1.5702 4.5831 -0.3883 C.3 1 <0> 0.1602
11 N1 1.6936 -0.3532 2.4034 N.ar 1 <0> -0.7482
12 N2 1.5430 -2.2738 3.8939 N.ar 1 <0> -0.7954
13 N3 -1.5407 -0.2138 3.9301 N.2 1 <0> -0.5448
14 N4 -0.3514 0.9698 2.4677 N.pl3 1 <0> -0.7037
15 N5 -0.3575 -2.7969 5.1783 N.pl3 1 <0> -0.9548
16 O1 0.6112 -0.1128 -2.5128 O.2 1 <0> -0.8309
17 O2 -4.0574 4.4134 -2.1284 O.2 1 <0> -0.8442
18 O3 -3.8745 3.1467 -5.2566 O.2 1 <0> -0.6607
19 O4 -2.4391 2.3385 -3.3431 O.2 1 <0> -0.6607
20 O5 -1.0663 2.9314 1.3403 O.3 1 <0> -0.4189
21 O6 1.8719 1.2205 0.0510 O.3 1 <0> -0.5838
22 O7 2.3704 1.8040 -2.5291 O.3 1 <0> -0.7592
23 O8 0.6744 1.7080 -4.3513 O.3 1 <0> -0.7592
24 O9 -2.9236 6.6121 -2.6571 O.3 1 <0> -0.7755
25 O10 -1.4478 2.8301 -5.5061 O.3 1 <0> -0.7746
26 O11 -0.0234 2.4102 -2.0766 O.3 1 <0> -0.5321
27 O12 -1.4691 4.8296 -1.7751 O.3 1 <0> -0.5795
28 O13 -2.3414 4.7222 -4.1460 O.3 1 <0> -0.7993
29 P1 0.8785 1.3189 -2.8048 P.3 1 <0> 1.6463
30 P2 -2.7955 5.0069 -2.6568 P.3 1 <0> 1.8005
31 S1 -2.6494 3.1882 -4.4913 S.o2 1 <0> 2.0120
32 H1 3.1690 -1.7765 2.7217 H 1 <0> 0.0543
33 H2 -2.3405 1.5628 3.0571 H 1 <0> 0.0844
34 H3 0.8798 3.4749 -0.5987 H 1 <0> 0.0940
35 H4 -0.0907 0.6143 -0.1192 H 1 <0> 0.0872
36 H5 -2.0161 2.4824 -0.4392 H 1 <0> 0.0943
37 H6 0.8460 2.5845 2.0490 H 1 <0> 0.1138
38 H7 -0.8786 5.2592 0.1270 H 1 <0> 0.0682
39 H8 -2.5680 4.8220 -0.0038 H 1 <0> 0.0682
40 H9 -1.1364 -2.3592 5.6576 H 1 <0> 0.4494
41 H10 0.2897 -3.3472 5.7261 H 1 <0> 0.4494
42 H11 2.0579 0.5287 0.7302 H 1 <0> 0.4358
43 H12 2.6155 1.5653 -1.6047 H 1 <0> 0.4872
44 H13 1.1983 1.0820 -4.8931 H 1 <0> 0.4872
45 H14 -3.8374 6.8877 -2.8585 H 1 <0> 0.4888
46 H15 -0.6675 2.5179 -4.9808 H 1 <0> 0.5095
@<TRIPOS>BOND
1 1 11 ar
2 1 12 ar
3 2 13 2
4 2 14 1
5 3 4 ar
6 3 5 ar
7 3 13 1
8 4 11 ar
9 4 14 1
10 5 12 ar
11 5 15 1
12 6 7 1
13 6 8 1
14 6 26 1
15 7 9 1
16 7 21 1
17 8 10 1
18 8 20 1
19 9 14 1
20 9 20 1
21 10 27 1
22 16 29 2
23 17 30 2
24 18 31 2
25 19 31 2
26 22 29 1
27 23 29 1
28 24 30 1
29 25 31 1
30 26 29 1
31 27 30 1
32 28 30 1
33 28 31 1
34 1 32 1
35 2 33 1
36 6 34 1
37 7 35 1
38 8 36 1
39 9 37 1
40 10 38 1
41 10 39 1
42 15 40 1
43 15 41 1
44 21 42 1
45 22 43 1
46 23 44 1
47 24 45 1
48 25 46 1
@<TRIPOS>MOLECULE
DrugBank_2592
46 48 0 0 0
SMALL
USER_CHARGES
[2] The XML-serialized OpenMM system
Summary
<?xml version="1.0" ?>
<System openmmVersion="7.3.1" type="System" version="1">
<PeriodicBoxVectors>
<A x="2" y="0" z="0"/>
<B x="0" y="2" z="0"/>
<C x="0" y="0" z="2"/>
</PeriodicBoxVectors>
<Particles>
<Particle mass="12.01078"/>
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<Particle mass="14.00672"/>
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<Particle mass="15.99943"/>
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<Particle mass="30.9737622"/>
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<Particle mass="32.0655"/>
<Particle mass="1.007947"/>
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</Particles>
<Constraints/>
<Forces>
<Force alpha="0" cutoff="1" dispersionCorrection="1" ewaldTolerance=".0005" forceGroup="0" ljAlpha="0" ljnx="0" ljny="0" ljnz="0" method="0" nx="0" ny="0" nz="0" recipForceGroup="-1" rfDielectric="78.3" switchingDistance="-1" type="NonbondedForce" useSwitchingFunction="0" version="3">
<GlobalParameters/>
<ParticleOffsets/>
<ExceptionOffsets/>
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<Angle a="1.911135530933791" k="585.76" p1="21" p2="28" p3="25"/>
<Angle a="1.911135530933791" k="585.76" p1="22" p2="28" p3="25"/>
<Angle a="1.911135530933791" k="585.76" p1="23" p2="29" p3="26"/>
<Angle a="1.911135530933791" k="585.76" p1="23" p2="29" p3="27"/>
<Angle a="1.911135530933791" k="502.08000000000004" p1="24" p2="30" p3="27"/>
<Angle a="1.911135530933791" k="418.40000000000003" p1="25" p2="5" p3="33"/>
<Angle a="1.911135530933791" k="418.40000000000003" p1="26" p2="9" p3="37"/>
<Angle a="1.911135530933791" k="418.40000000000003" p1="26" p2="9" p3="38"/>
<Angle a="1.911135530933791" k="585.76" p1="26" p2="29" p3="27"/>
<Angle a="1.9722220547535925" k="418.40000000000003" p1="28" p2="21" p3="42"/>
<Angle a="1.9722220547535925" k="418.40000000000003" p1="28" p2="22" p3="43"/>
<Angle a="1.9722220547535925" k="418.40000000000003" p1="29" p2="23" p3="44"/>
<Angle a="1.9722220547535925" k="418.40000000000003" p1="29" p2="27" p3="30"/>
<Angle a="1.9722220547535925" k="418.40000000000003" p1="30" p2="24" p3="45"/>
<Angle a="1.911135530933791" k="292.88" p1="37" p2="9" p3="38"/>
<Angle a="2.0943951023931953" k="418.40000000000003" p1="39" p2="14" p3="40"/>
</Angles>
</Force>
<Force forceGroup="0" type="HarmonicBondForce" usesPeriodic="0" version="2">
<Bonds>
<Bond d=".134" k="401664" p1="0" p2="10"/>
<Bond d=".134" k="401664" p1="0" p2="11"/>
<Bond d=".10800000000000001" k="307105.6" p1="0" p2="31"/>
<Bond d=".13" k="443504" p1="1" p2="12"/>
<Bond d=".13799999999999998" k="357313.6" p1="1" p2="13"/>
<Bond d=".10800000000000001" k="307105.6" p1="1" p2="32"/>
<Bond d=".13999999999999999" k="392459.19999999995" p1="2" p2="3"/>
<Bond d=".13999999999999999" k="392459.19999999995" p1="2" p2="4"/>
<Bond d=".13899999999999998" k="343088" p1="2" p2="12"/>
<Bond d=".134" k="401664" p1="3" p2="10"/>
<Bond d=".13799999999999998" k="357313.6" p1="3" p2="13"/>
<Bond d=".134" k="401664" p1="4" p2="11"/>
<Bond d=".13799999999999998" k="357313.6" p1="4" p2="14"/>
<Bond d=".1526" k="259408" p1="5" p2="6"/>
<Bond d=".1526" k="259408" p1="5" p2="7"/>
<Bond d=".137" k="267776" p1="5" p2="25"/>
<Bond d=".10900000000000001" k="284512" p1="5" p2="33"/>
<Bond d=".1526" k="259408" p1="6" p2="8"/>
<Bond d=".141" k="267776" p1="6" p2="20"/>
<Bond d=".10900000000000001" k="284512" p1="6" p2="34"/>
<Bond d=".1526" k="259408" p1="7" p2="9"/>
<Bond d=".137" k="267776" p1="7" p2="19"/>
<Bond d=".10900000000000001" k="284512" p1="7" p2="35"/>
<Bond d=".147" k="307105.6" p1="8" p2="13"/>
<Bond d=".137" k="267776" p1="8" p2="19"/>
<Bond d=".10900000000000001" k="284512" p1="8" p2="36"/>
<Bond d=".137" k="267776" p1="9" p2="26"/>
<Bond d=".10900000000000001" k="284512" p1="9" p2="37"/>
<Bond d=".10900000000000001" k="284512" p1="9" p2="38"/>
<Bond d=".101" k="363171.19999999995" p1="14" p2="39"/>
<Bond d=".101" k="363171.19999999995" p1="14" p2="40"/>
<Bond d=".148" k="439320" p1="15" p2="28"/>
<Bond d=".148" k="439320" p1="16" p2="29"/>
<Bond d=".144" k="251040" p1="17" p2="30"/>
<Bond d=".144" k="251040" p1="18" p2="30"/>
<Bond d=".096" k="462750.39999999997" p1="20" p2="41"/>
<Bond d=".16100000000000003" k="192464" p1="21" p2="28"/>
<Bond d=".096" k="462750.39999999997" p1="21" p2="42"/>
<Bond d=".16100000000000003" k="192464" p1="22" p2="28"/>
<Bond d=".096" k="462750.39999999997" p1="22" p2="43"/>
<Bond d=".16100000000000003" k="192464" p1="23" p2="29"/>
<Bond d=".096" k="462750.39999999997" p1="23" p2="44"/>
<Bond d=".15960000000000002" k="251040" p1="24" p2="30"/>
<Bond d=".096" k="462750.39999999997" p1="24" p2="45"/>
<Bond d=".16100000000000003" k="192464" p1="25" p2="28"/>
<Bond d=".16100000000000003" k="192464" p1="26" p2="29"/>
<Bond d=".16100000000000003" k="192464" p1="27" p2="29"/>
<Bond d=".15960000000000002" k="251040" p1="27" p2="30"/>
</Bonds>
</Force>
</Forces>
</System>
Right, that was the other thing I was forgetting: We had crashes with GAFF, too, when simulating sulfonic acids in such environments.
I had thought we'd not have crashes with SMIRNOFF due to having a nonzero LJ paraeters on hydroxyl hydrogens, but I'd have to check if the hydroxyl LJ parameters get applied here.
Why do H11 through H15 have Lennard-Jones epsilon parameters that are several orders of magnitude smaller than everything else?
<Particle eps=".0002204968" q=".4357999861240387" sig=".053453923088420355"/>
<Particle eps=".0002204968" q=".487199991941452" sig=".053453923088420355"/>
<Particle eps=".0002204968" q=".487199991941452" sig=".053453923088420355"/>
<Particle eps=".0002204968" q=".4887999892234802" sig=".053453923088420355"/>
<Particle eps=".0002204968" q=".5095000267028809" sig=".053453923088420355"/>
These appear to be hydrogens on the phosphates.
@j-wags : If you have a script to reproduce this, perhaps you can just try making the eps larger for these (say 0.065) and see if they still crash at 2 fs?
@jchodera see SMIRNOFF paper SI section 3 . These are small because AMBER formerly had them as zero, and for smirnoff99Frosst we essentially made them just nonzero enough to remove crashes without significantly perturbing densities, etc. The plan was/is to refit these values when doing condensed phase properties -- it's likely they should be larger, but would have perturbed MANY properties if we'd made them larger without doing a refit of other parameters at the same time.
It is possible that these only are large enough to remove crashes when in proximity to typical oxygens and in phosphate environments there are other differences which mean the crashes are still there. I doubt it though; I expect the issue is more that the wonky angle results in really weird geometries which have very rough energy landscapes and encounter large forces even after only very small perturbations.
(For what it's worth, for the paper I was actually able to use OpenMM to compute the energy landscape for pulling two neutral acids -- acetic acid IIRC -- together in a dimer (subtracting out the restraint energy) and showed that with typical AMBER parameters, the energy becomes infinite and negative as the proton approaches the other oxygen, and the barrier was not that large, so such "fusion" of acid dimers would not be uncommon in simulations -- consistent with what Chris and I had observed before. I found that adding even a small nonzero parameter here removed those issues entirely.)
It is possible that these only are large enough to remove crashes when in proximity to typical oxygens and in phosphate environments there are other differences which mean the crashes are still there. I doubt it though; I expect the issue is more that the wonky angle results in really weird geometries which have very rough energy landscapes and encounter large forces even after only very small perturbations.
Should be easy to test if @j-wags can post his test code.
Sorry, got caught up in a few other things.
Reproducing test code:
from openforcefield.topology import Molecule, Topology
from openforcefield.typing.engines.smirnoff import ForceField
from openforcefield.utils import get_data_file_path
offmol = Molecule('DB2592_minIssue_conf1.mol2')
off_top = Topology.from_molecules([offmol])
ff = ForceField(get_data_file_path('test_forcefields/smirnoff99Frosst.offxml'))
omm_system = ff.create_openmm_system(off_top, charge_from_molecules=[offmol])
from simtk import openmm, unit
# Propagate the System with Langevin dynamics.
time_step = 2*unit.femtoseconds # simulation timestep
temperature = 300*unit.kelvin # simulation temperature
friction = 1/unit.picosecond # collision rate
integrator = openmm.LangevinIntegrator(temperature, friction, time_step)
# Length of the simulation.
num_steps = 1000 # number of integration steps to run
# Logging options.
trj_freq = 1 # number of steps per written trajectory frame
data_freq = 1 # number of steps per written simulation statistics
# Set up an OpenMM simulation.
omm_topology = off_top.to_openmm()
simulation = openmm.app.Simulation(omm_topology, omm_system, integrator)
# Set the initial positions.
#positions = pdbfile.getPositions()
simulation.context.setPositions(offmol.conformers[0])
# Randomize the velocities from a Boltzmann distribution at a given temperature.
simulation.context.setVelocitiesToTemperature(temperature)
# Configure the information in the output files.
pdb_reporter = openmm.app.PDBReporter('trajectory.pdb', trj_freq)
state_data_reporter = openmm.app.StateDataReporter('data.csv', data_freq, step=True,
potentialEnergy=True, temperature=True,
density=True)
simulation.reporters.append(pdb_reporter)
simulation.reporters.append(state_data_reporter)
# Run the simulation
simulation.step(num_steps)
Contents of DB2592_minIssue_conf1.mol2 are posted in my previous comment (just the first conformer from the molecules posted in the original issue)
This is quite old and may be resolved in the several generations of force field development of the past four years, so I'm closing it now. If there are new issues with these chemistries they can be reported here or at https://github.com/orgs/openforcefield/discussions
