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AmberTools19 compute_partial_charges_am1bcc fails on acetate #532

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j-wags opened this issue Feb 28, 2020 · 10 comments · Fixed by #471
Closed

AmberTools19 compute_partial_charges_am1bcc fails on acetate #532

j-wags opened this issue Feb 28, 2020 · 10 comments · Fixed by #471
Milestone
0.7.0

Comments

@j-wags
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j-wags commented Feb 28, 2020

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
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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
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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
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pandoc                    2.7.3                         0    conda-forge
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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
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pip                       19.2.3                   py37_0    conda-forge
pixman                    0.38.0            h01d97ff_1003    conda-forge
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pyarrow                   0.13.0           py37he1943e6_2    conda-forge
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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
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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
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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
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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
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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
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wcwidth                   0.1.7                      py_1    conda-forge
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wheel                     0.33.6                   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.
@jaimergp
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While there's no antechamber --version we can parse, they do have different help messages we can parse to distinguish them. Notice the first line:

antechamber -h in ambermini:

antechamber -h                                                                                                                
Usage: antechamber -i   input file name
                   -fi  input file format
                   -o   output file name
                   -fo  output file format
                   -c   charge method
                   -cf  charge file name
                   -nc  net molecular charge (int)
                   -a   additional file name
                   -fa  additional file format
                   -ao  additional file operation
                        crd   : only read in coordinate
                        crg   : only read in charge
                        radius: only read in radius
                        name  : only read in atom name
                        type  : only read in atom type
                        bond  : only read in bond type
                   -m   multiplicity (2S+1), default is 1
                   -rn  residue name, overrides input file, default is MOL
...

antechamber in ambertools==19:

antechamber -h              
Welcome to antechamber 19.0: molecular input file processor.

Usage: antechamber -i   input file name
                   -fi  input file format
                   -o   output file name
                   -fo  output file format
                   -c   charge method
                   -cf  charge file name
                   -nc  net molecular charge (int)
                   -a   additional file name
                   -fa  additional file format
                   -ao  additional file operation
                        crd   : only read in coordinate
                        crg   : only read in charge
                        radius: only read in radius
                        name  : only read in atom name
                        type  : only read in atom type
                        bond  : only read in bond type
                   -m   multiplicity (2S+1), default is 1
                   -rn  residue name, overrides input file, default is MOL
                   -rf  residue toplogy file name in prep input file,
                        default is molecule.res
                   -ch  check file name for gaussian, default is 'molecule'
                   -ek  mopac or sqm keyword, inside quotes; overwrites previous ones
                   -gk  gaussian job keyword, inside quotes

@j-wags j-wags changed the title AmberTools19 compute_partial_charges fails on acetate AmberTools19 compute_partial_charges_am1bcc fails on acetate Feb 28, 2020
@j-wags
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j-wags commented Feb 28, 2020

Hm, I'm realizing that, with the addition of WBO calculations in AmberToolsToolkitWrapper (#508), as well as the antechamber API changes in this issue, we might not WANT to provide support for AmberMini (which is based on AmberTools16) in our next release. Trying to support both would involve

  • detecting which AT version we're working with using something like @jaimergp proposed above
  • Changing the behavior of compute_partial_charges_am1bcc depending on which version of AT is present
  • Failing with an informative error if people try to compute WBOs with AmberMini (since those weren't included until AT19)

Forcing all users to upgrade to AT19 would be a bit painful up front, but on the other hand, it would help with things like #130 (which can only be solved with an AT upgrade). Thoughts?

@SimonBoothroyd
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+1 on dropping support for AmberTools < 19 - it seems the maintenance overhead added by trying to support both would not be worth the effort, and migrating to 19 would provide significant benefits.

If this causes significant issues for users, they could always implement their own subclass of AmberToolsToolkitWrapper which uses older amber versions and use that in place of the default. If enough users complain, this could be added to the toolkit directly but probably isn't worth the effort unless many complaints appear on the issue tracker.

@davidlmobley
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Yes, agree relating to force an upgrade. We should require the more recent version.

@j-wags j-wags mentioned this issue Feb 28, 2020
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@jaimergp
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Maybe a deprecation warning in an intermediate release?

@jaimergp
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This reminds me that I should also add a run_constrained: ambermini=999999 to the CF ambertools package to avoid having both installed in the same environment.

I can do this now or as part of the AT 20 release.

@j-wags
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j-wags commented Feb 28, 2020 •
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I can do this now or as part of the AT 20 release.

Oh, it's awesome that you can make them mutually exclusive.

OFFTK 0.7.0 will miss its next-monday deadline, so accounting for conference travel, it will likely be out mid-March. So, if you could have the latest ambertools package built with the ambermini exclusion by March 15, that would be great for our timeline. (it's not important whether that's AT19 or AT20, just whatever the default conda install will pull)

@j-wags
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j-wags commented Feb 28, 2020

Maybe a deprecation warning in an intermediate release?

I'd be OK with an informative error, but I'm not sure about a deprecation warning, since then we still have to do all of the work of supporting both versions simultaneously.

Don't get me wrong -- We do add deprecation warnings -- we're even adding some for compute_partial_charges_am1bcc in the coming 0.7.0 release. I just think that we can save a lot of time here by not trying to support both AmberTools versions simultaneously.

@jchodera
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jchodera commented Mar 1, 2020

I jumped the gun on this and switched the openforcefield recipe from ambermini to ambertools on Jan 25. We can additionally pin to ambertools>=19 if you want!

We might only use acdoctor to get more information to include in an exception if the antechamber call fails for some reason.

@j-wags
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j-wags commented Mar 2, 2020

No worries! We didn't have a test that triggered this behavior until now, so I'm also to blame (heck, it's on me that we were missing the test in the first place, and ALSO I approved the PR for the switch).

@j-wags j-wags added this to the 0.7.0 milestone Mar 10, 2020
@j-wags j-wags mentioned this issue Mar 12, 2020
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@j-wags j-wags mentioned this issue Apr 21, 2020
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@j-wags j-wags mentioned this issue Aug 13, 2020
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Add ChargeIncrementModelHandler openforcefield/openff-toolkit
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@jaimergp @jchodera @davidlmobley @j-wags @SimonBoothroyd