AmberTools19 compute_partial_charges_am1bcc fails on acetate #532
Description
Describe the bug
toolkit_registry = ToolkitRegistry(toolkit_precedence=[AmberToolsToolkitWrapper, RDKitToolkitWrapper])
molecule = Molecule.from_smiles('CC(=O)[O-]')
molecule.compute_partial_charges_am1bcc(toolkit_registry=toolkit_registry)
Output
Antechamber complains about the central carbon only having three bonds
Solution
Turn acdoctor off using -dr n command line arguments.
Similar issue is listed here: http://archive.ambermd.org/201705/0020.html
One complication is that this may not work with AmberMini, since acdoctor wasn't bundled into antechamber until recently.
Computing environment (please complete the following information):
MacOS X
(off-dev) jwagner@MBP-S$ conda list
# packages in environment at /Users/jwagner/miniconda3/envs/off-dev:
#
# Name Version Build Channel
alabaster 0.7.12 py_0 conda-forge
ambertools 18.0 0 omnia
appnope 0.1.0 py37_1000 conda-forge
arrow-cpp 0.13.0 py37h43d7656_7 conda-forge
asn1crypto 1.0.1 py37_0 conda-forge
atomicwrites 1.3.0 py_0 conda-forge
attrs 19.2.0 py_0 conda-forge
babel 2.7.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
bleach 3.1.0 py_0 conda-forge
boost 1.70.0 py37haf112f3_1 conda-forge
boost-cpp 1.70.0 h75728bb_2 conda-forge
brotli 1.0.7 h6de7cb9_1000 conda-forge
bson 0.5.8 py_0 conda-forge
bzip2 1.0.8 h01d97ff_1 conda-forge
ca-certificates 2019.11.28 hecc5488_0 conda-forge
cairo 1.16.0 he1c11cd_1002 conda-forge
certifi 2019.11.28 py37_0 conda-forge
cffi 1.12.3 py37hccf1714_0 conda-forge
chardet 3.0.4 py37_1003 conda-forge
codecov 2.0.15 py_1 conda-forge
coverage 5.0.2 py37h0b31af3_0 conda-forge
cryptography 2.7 py37h212c5bf_0 conda-forge
cython 0.29.13 py37h6de7cb9_0 conda-forge
dbus 1.13.6 h2f22bb5_0 conda-forge
decorator 4.4.0 py_0 conda-forge
defusedxml 0.6.0 py_0 conda-forge
docutils 0.15.2 py37_0 conda-forge
double-conversion 3.1.5 h4a8c4bd_2 conda-forge
entrypoints 0.3 py37_1000 conda-forge
expat 2.2.5 h6de7cb9_1003 conda-forge
fftw3f 3.3.4 2 omnia
fontconfig 2.13.1 h6b1039f_1001 conda-forge
freetype 2.10.0 h24853df_1 conda-forge
gettext 0.19.8.1 h46ab8bc_1002 conda-forge
gflags 2.2.2 h4a8c4bd_1002 conda-forge
glib 2.58.3 h9d45998_1002 conda-forge
glog 0.4.0 h6de7cb9_1 conda-forge
h5py 2.10.0 nompi_py37h106b333_101 conda-forge
hdf5 1.10.5 nompi_h3e39495_1104 conda-forge
icu 64.2 h6de7cb9_1 conda-forge
idna 2.8 py37_1000 conda-forge
imagesize 1.1.0 py_0 conda-forge
importlib_metadata 0.23 py37_0 conda-forge
ipykernel 5.1.2 py37h5ca1d4c_0 conda-forge
ipython 7.8.0 py37h5ca1d4c_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.5.1 py_0 conda-forge
jedi 0.15.1 py37_0 conda-forge
jinja2 2.10.3 py_0 conda-forge
jpeg 9c h1de35cc_1001 conda-forge
jsonschema 3.1.1 py37_0 conda-forge
jupyter 1.0.0 py_2 conda-forge
jupyter_client 5.3.3 py37_1 conda-forge
jupyter_console 6.0.0 py_0 conda-forge
jupyter_core 4.5.0 py_0 conda-forge
libblas 3.8.0 13_openblas conda-forge
libcblas 3.8.0 13_openblas conda-forge
libclang 8.0.1 h770b8ee_1 conda-forge
libcxx 9.0.0 0 conda-forge
libcxxabi 9.0.0 0 conda-forge
libevent 2.1.10 hafa8578_0 conda-forge
libffi 3.2.1 h6de7cb9_1006 conda-forge
libgcc 4.8.5 1 conda-forge
libgfortran 4.0.0 2 conda-forge
libiconv 1.15 h01d97ff_1005 conda-forge
liblapack 3.8.0 13_openblas conda-forge
libllvm8 8.0.1 h770b8ee_0 conda-forge
libopenblas 0.3.7 h4bb4525_1 conda-forge
libpng 1.6.37 h2573ce8_0 conda-forge
libprotobuf 3.8.0 hfbae3c0_0 conda-forge
libsodium 1.0.17 h01d97ff_0 conda-forge
libtiff 4.0.10 hd08fb8f_1003 conda-forge
libxml2 2.9.9 h12c6b28_5 conda-forge
llvm-openmp 9.0.0 h40edb58_0 conda-forge
lz4-c 1.8.3 h6de7cb9_1001 conda-forge
m2r 0.2.1 py_0 conda-forge
markupsafe 1.1.1 py37h1de35cc_0 conda-forge
mistune 0.8.4 py37h1de35cc_1000 conda-forge
more-itertools 7.2.0 py_0 conda-forge
msgpack-python 0.6.2 py37h770b8ee_0 conda-forge
nbconvert 5.6.0 py37_1 conda-forge
nbformat 4.4.0 py_1 conda-forge
nbsphinx 0.4.3 py_0 conda-forge
nbval 0.9.4 py_0 conda-forge
ncurses 6.1 h0a44026_1002 conda-forge
networkx 2.4 py_0 conda-forge
nglview 2.7.1 pyh5ca1d4c_0 conda-forge
notebook 6.0.1 py37_0 conda-forge
nspr 4.20 h0a44026_1000 conda-forge
nss 3.46 hcec2283_0 conda-forge
numpy 1.17.2 py37h6b0580a_0 conda-forge
numpydoc 0.9.1 py_0 conda-forge
olefile 0.46 py_0 conda-forge
openeye-toolkits 2019.10.2 py37_0 openeye
openforcefield 0.5.1+9.gd2e7173.dirty dev_0 <develop>
openforcefields 1.0.0 py37_0 omnia
openmm 7.4.1 py37_cuda101_rc_1 omnia
openssl 1.1.1d h0b31af3_0 conda-forge
packaging 19.2 py_0 conda-forge
pandas 0.25.1 py37h86efe34_0 conda-forge
pandoc 2.7.3 0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
parmed 3.2.0 py37_0 omnia
parquet-cpp 1.5.1 2 conda-forge
parso 0.5.1 py_0 conda-forge
pcre 8.41 h4a8c4bd_1004 conda-forge
pexpect 4.7.0 py37_0 conda-forge
pickleshare 0.7.5 py37_1000 conda-forge
pillow 6.2.0 py37hb6f49c9_0 conda-forge
pint 0.10.1 py_0 conda-forge
pip 19.2.3 py37_0 conda-forge
pixman 0.38.0 h01d97ff_1003 conda-forge
plotly 4.5.0 py_0 conda-forge
pluggy 0.13.0 py37_0 conda-forge
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prompt_toolkit 2.0.10 py_0 conda-forge
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ptyprocess 0.6.0 py_1001 conda-forge
py 1.8.0 py_0 conda-forge
py-cpuinfo 5.0.0 py_0 conda-forge
pyarrow 0.13.0 py37he1943e6_2 conda-forge
pycairo 1.18.1 py37h650f75e_0 conda-forge
pycparser 2.19 py37_1 conda-forge
pydantic 1.4 py37h0b31af3_0 conda-forge
pygments 2.4.2 py_0 conda-forge
pyopenssl 19.0.0 py37_0 conda-forge
pyparsing 2.4.2 py_0 conda-forge
pyqt 5.12.3 py37h2a560b1_0 conda-forge
pyqt5-sip 4.19.18 pypi_0 pypi
pyqtwebengine 5.12.1 pypi_0 pypi
pyrsistent 0.15.4 py37h01d97ff_0 conda-forge
pysocks 1.7.1 py37_0 conda-forge
pytest 5.3.2 py37_0 conda-forge
pytest-cov 2.8.1 py_0 conda-forge
python 3.7.3 h93065d6_1 conda-forge
python-dateutil 2.8.0 py_0 conda-forge
pytz 2019.3 py_0 conda-forge
pyyaml 5.1.2 py37h01d97ff_0 conda-forge
pyzmq 18.1.0 py37hee98d25_0 conda-forge
qcelemental 0.13.0 py_0 conda-forge
qcengine 0.13.0 py_0 conda-forge
qcportal 0.13.0 py_0 conda-forge
qt 5.12.5 h1b46049_0 conda-forge
qtconsole 4.5.5 py_0 conda-forge
rdkit 2019.03.4 py37h3471270_1 conda-forge
re2 2020.01.01 h4a8c4bd_0 conda-forge
readline 8.0 hcfe32e1_0 conda-forge
requests 2.22.0 py37_1 conda-forge
retrying 1.3.3 py_2 conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 41.4.0 py37_0 conda-forge
six 1.12.0 py37_1000 conda-forge
smirnoff99frosst 1.1.0 py37_1 omnia
snappy 1.1.7 h4a8c4bd_1003 conda-forge
snowballstemmer 2.0.0 py_0 conda-forge
sphinx 2.2.1 py_0 conda-forge
sphinx_bootstrap_theme 0.6.4 py_0 conda-forge
sphinxcontrib-applehelp 1.0.1 py_0 conda-forge
sphinxcontrib-devhelp 1.0.1 py_0 conda-forge
sphinxcontrib-htmlhelp 1.0.2 py_0 conda-forge
sphinxcontrib-jsmath 1.0.1 py_0 conda-forge
sphinxcontrib-qthelp 1.0.2 py_0 conda-forge
sphinxcontrib-serializinghtml 1.1.3 py_0 conda-forge
sqlite 3.30.1 h93121df_0 conda-forge
terminado 0.8.2 py37_0 conda-forge
testpath 0.4.2 py_1001 conda-forge
thrift-cpp 0.12.0 h874095a_1004 conda-forge
tk 8.6.9 h2573ce8_1003 conda-forge
toml 0.10.0 py_0 conda-forge
tornado 6.0.3 py37h01d97ff_0 conda-forge
tqdm 4.42.1 py_0 conda-forge
traitlets 4.3.3 py37_0 conda-forge
urllib3 1.25.6 py37_0 conda-forge
wcwidth 0.1.7 py_1 conda-forge
webencodings 0.5.1 py_1 conda-forge
wheel 0.33.6 py37_0 conda-forge
widgetsnbextension 3.5.1 py37_0 conda-forge
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xz 5.2.4 h1de35cc_1001 conda-forge
yaml 0.1.7 h1de35cc_1001 conda-forge
zeromq 4.3.2 h6de7cb9_2 conda-forge
zipp 0.6.0 py_0 conda-forge
zlib 1.2.11 h0b31af3_1006 conda-forge
zstd 1.4.0 ha9f0a20_0 conda-forge
Additional context
Add any other context about the problem here.