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Parameter assignment not preserving original residue labels and numbers
See original GitHub issueDescribe the bug
Not really sure if this falls under the bug category, but still an issue I was running into. When assigning parameters using the parameter assignment example (examples/using_smirnoff_in_amber_or_gromacs/export_with_interchange.ipynb) the resulting .top and .gro files don’t have the correct residue labels and numbers from the input .pdb file. Instead, the residue labels default to the pdb file name (mop_hexamer_mbuild.pdb).
To Reproduce I attached a .zip with the files I used to run into this issue. The jupyter-notebook should be setup to read in the .mol and .pdb files used to generate the OpenFF parameters. One note here, I modified my OpenEye installation to allow for AM1BCC parameterization of molecules with 300+ atoms, but that shouldn’t be an issue since this molecule has 285 atoms.
Output The original pdb file had residue labels and residue numbers:
CRYST1 26.819 22.979 24.130 90.00 90.00 90.00 P 1
HETATM 1 C HEX 1 -3.002 -4.911 0.117 0.00 0.00 C
HETATM 2 O HEX 1 -3.879 -5.407 -0.639 0.00 0.00 O
HETATM 3 C HEX 1 -2.717 -3.465 0.106 0.00 0.00 C
HETATM 4 C HEX 1 -1.735 -2.945 0.961 0.00 0.00 C
HETATM 5 C HEX 1 -1.450 -1.577 0.963 0.00 0.00 C
HETATM 6 C HEX 1 -2.138 -0.707 0.101 0.00 0.00 C
HETATM 7 C HEX 1 -1.831 0.744 0.093 0.00 0.00 C
HETATM 8 C HEX 1 -0.513 1.234 -0.091 0.00 0.00 C
HETATM 9 C HEX 1 -0.275 2.617 -0.011 0.00 0.00 C
HETATM 10 C HEX 1 -1.319 3.517 0.222 0.00 0.00 C
HETATM 11 O HEX 1 -1.017 4.885 0.285 0.00 0.00 O
HETATM 12 C HEX 1 -1.977 5.912 0.514 0.00 0.00 C
HETATM 13 C HEX 1 -2.626 3.026 0.380 0.00 0.00 C
HETATM 14 C HEX 1 -2.876 1.655 0.315 0.00 0.00 C
HETATM 15 C HEX 1 0.623 0.335 -0.408 0.00 0.00 C
HETATM 16 C HEX 1 0.558 -0.531 -1.510 0.00 0.00 C
HETATM 17 C HEX 1 1.624 -1.385 -1.798 0.00 0.00 C
HETATM 18 C HEX 1 2.767 -1.377 -0.995 0.00 0.00 C
HETATM 19 C HEX 1 2.858 -0.506 0.107 0.00 0.00 C
HETATM 20 C HEX 1 1.779 0.350 0.390 0.00 0.00 C
HETATM 21 C HEX 1 4.092 -0.490 0.994 0.00 0.00 C
HETATM 22 N HEX 1 4.278 -1.776 1.670 0.00 0.00 N
HETATM 23 C HEX 1 5.349 -0.118 0.201 0.00 0.00 C
HETATM 24 C HEX 1 -3.130 -1.225 -0.746 0.00 0.00 C
HETATM 25 C HEX 1 -3.416 -2.593 -0.747 0.00 0.00 C
HETATM 26 H HEX 1 -1.188 -3.599 1.631 0.00 0.00 H
HETATM 27 H HEX 1 -0.695 -1.196 1.639 0.00 0.00 H
HETATM 28 H HEX 1 0.728 3.003 -0.153 0.00 0.00 H
HETATM 29 H HEX 1 -1.463 6.895 0.515 0.00 0.00 H
HETATM 30 H HEX 1 -2.465 5.765 1.501 0.00 0.00 H
HETATM 31 H HEX 1 -2.739 5.909 -0.294 0.00 0.00 H
HETATM 32 H HEX 1 -3.456 3.696 0.561 0.00 0.00 H
HETATM 33 H HEX 1 -3.889 1.300 0.462 0.00 0.00 H
HETATM 34 H HEX 1 -0.317 -0.545 -2.148 0.00 0.00 H
HETATM 35 H HEX 1 1.565 -2.054 -2.646 0.00 0.00 H
HETATM 36 H HEX 1 3.579 -2.050 -1.237 0.00 0.00 H
HETATM 37 H HEX 1 1.828 1.017 1.242 0.00 0.00 H
HETATM 38 H HEX 1 3.972 0.289 1.781 0.00 0.00 H
HETATM 39 H HEX 1 3.417 -1.991 2.223 0.00 0.00 H
HETATM 40 H HEX 1 5.583 -0.888 -0.563 0.00 0.00 H
HETATM 41 H HEX 1 6.216 -0.033 0.890 0.00 0.00 H
HETATM 42 H HEX 1 5.205 0.861 -0.304 0.00 0.00 H
HETATM 43 H HEX 1 -3.672 -0.570 -1.418 0.00 0.00 H
HETATM 44 H HEX 1 -4.180 -2.968 -1.416 0.00 0.00 H
HETATM 45 C HEX 2 5.574 -2.424 1.281 0.00 0.00 C
HETATM 46 O HEX 2 6.273 -2.373 0.234 0.00 0.00 O
HETATM 47 C HEX 2 5.705 -3.544 2.231 0.00 0.00 C
HETATM 48 C HEX 2 4.912 -3.568 3.388 0.00 0.00 C
HETATM 49 C HEX 2 5.021 -4.622 4.298 0.00 0.00 C
But in the topology file the residue name and numbers are all set to 1 and the original pdb name.
[ atoms ]
;num, type, resnum, resname, atomname, cgnr, q, m
1 C1 1 mop_hexamer_mbuild.pdb1 C1 1 0.64525998 12.01078000
2 O1 1 mop_hexamer_mbuild.pdb1 O1 2 -0.54570001 15.99943000
3 C2 1 mop_hexamer_mbuild.pdb1 C2 3 -0.13563999 12.01078000
4 C3 1 mop_hexamer_mbuild.pdb1 C3 4 -0.07675000 12.01078000
5 C4 1 mop_hexamer_mbuild.pdb1 C4 5 -0.13117000 12.01078000
6 C5 1 mop_hexamer_mbuild.pdb1 C5 6 0.00266000 12.01078000
Computing environment (please complete the following information):
- Operating system: Ubuntu 20.04.5 LTS
- Output of running
conda list
# packages in environment at /home/tfobe/anaconda3/envs/terphenyl:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alchemlyb 0.6.0 pyhd8ed1ab_0 conda-forge
amberlite 16.0 pypi_0 pypi
ambertools 21.9 py39h69e27f8_0 conda-forge
amberutils 21.0 pypi_0 pypi
analyze-foldamers 0+untagged.264.g8f9458a dev_0 <develop>
anyio 3.6.1 pypi_0 pypi
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py39hb9d737c_2 conda-forge
arpack 3.7.0 hdefa2d7_2 conda-forge
asttokens 2.0.5 pyhd8ed1ab_0 conda-forge
astunparse 1.6.3 pyhd8ed1ab_0 conda-forge
attrs 21.4.0 pyhd8ed1ab_0 conda-forge
babel 2.10.2 pypi_0 pypi
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
backports.zoneinfo 0.2.1 py39hb9d737c_5 conda-forge
beautifulsoup4 4.11.1 pyha770c72_0 conda-forge
biopython 1.79 py39hb9d737c_2 conda-forge
bleach 5.0.0 pyhd8ed1ab_0 conda-forge
blosc 1.21.1 h83bc5f7_3 conda-forge
boost 1.74.0 py39h5472131_5 conda-forge
boost-cpp 1.74.0 h75c5d50_8 conda-forge
brotli 1.0.9 h166bdaf_7 conda-forge
brotli-bin 1.0.9 h166bdaf_7 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2022.9.14 ha878542_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.16.0 ha61ee94_1011 conda-forge
certifi 2022.9.14 pyhd8ed1ab_0 conda-forge
cffi 1.15.0 py39h4bc2ebd_0 conda-forge
cftime 1.6.1 py39hd257fcd_0 conda-forge
charset-normalizer 2.0.12 pypi_0 pypi
chemcoord 2.0.5 pypi_0 pypi
click 8.1.3 py39hf3d152e_0 conda-forge
colorama 0.4.4 pyh9f0ad1d_0 conda-forge
cudatoolkit 11.7.0 hd8887f6_10 conda-forge
curl 7.83.1 h2283fc2_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cython 0.29.30 py39h5a03fae_0 conda-forge
debugpy 1.6.0 py39h5a03fae_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
ele 0.2.0 pyhd8ed1ab_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.0.0rc9 pyhd8ed1ab_0 conda-forge
executing 0.8.3 pyhd8ed1ab_0 conda-forge
expat 2.4.8 h27087fc_0 conda-forge
fasteners 0.17.3 pyhd8ed1ab_0 conda-forge
fftw 3.3.10 nompi_h77c792f_102 conda-forge
flit-core 3.7.1 pyhd8ed1ab_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.0 h8e229c2_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
future 0.18.2 pypi_0 pypi
gettext 0.19.8.1 h73d1719_1008 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
greenlet 1.1.2 py39h5a03fae_2 conda-forge
griddataformats 1.0.1 pyhd8ed1ab_0 conda-forge
gsd 2.6.0 py39hd257fcd_0 conda-forge
h5py 3.7.0 nompi_py39h63b1161_100 conda-forge
hdf4 4.2.15 h10796ff_3 conda-forge
hdf5 1.12.1 nompi_h4df4325_104 conda-forge
heteropolymer-simulations 0+untagged.103.g18607ba.dirty dev_0 <develop>
hypothesis 6.54.4 pyhd8ed1ab_0 conda-forge
icu 70.1 h27087fc_0 conda-forge
idna 3.3 pypi_0 pypi
importlib-metadata 4.11.4 py39hf3d152e_0 conda-forge
importlib_resources 5.7.1 pyhd8ed1ab_1 conda-forge
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge
ipykernel 6.14.0 pypi_0 pypi
ipython 8.4.0 py39hf3d152e_0 conda-forge
ipython-genutils 0.2.0 pypi_0 pypi
ipython_genutils 0.2.0 py_1 conda-forge
jbig 2.1 h7f98852_2003 conda-forge
jedi 0.18.1 py39hf3d152e_1 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
joblib 1.1.0 pyhd8ed1ab_0 conda-forge
jpeg 9e h166bdaf_1 conda-forge
json5 0.9.8 pypi_0 pypi
jsonschema 4.6.0 pyhd8ed1ab_0 conda-forge
jupyter-server 1.17.1 pypi_0 pypi
jupyter_client 7.3.4 pyhd8ed1ab_0 conda-forge
jupyter_core 4.10.0 py39hf3d152e_0 conda-forge
jupyterlab 3.4.3 pypi_0 pypi
jupyterlab-server 2.14.0 pypi_0 pypi
jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.2 py39hf939315_1 conda-forge
krb5 1.19.3 h08a2579_0 conda-forge
latexcodec 2.0.1 pypi_0 pypi
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libblas 3.9.0 14_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_7 conda-forge
libbrotlidec 1.0.9 h166bdaf_7 conda-forge
libbrotlienc 1.0.9 h166bdaf_7 conda-forge
libcblas 3.9.0 14_linux64_openblas conda-forge
libcurl 7.83.1 h2283fc2_0 conda-forge
libdeflate 1.10 h7f98852_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 12.1.0 h8d9b700_16 conda-forge
libgfortran-ng 12.1.0 h69a702a_16 conda-forge
libgfortran5 12.1.0 hdcd56e2_16 conda-forge
libglib 2.70.2 h174f98d_4 conda-forge
libgomp 12.1.0 h8d9b700_16 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 14_linux64_openblas conda-forge
libnetcdf 4.8.1 nompi_h329d8a1_102 conda-forge
libnghttp2 1.47.0 he49606f_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.20 pthreads_h78a6416_0 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libprotobuf 3.20.1 h6239696_0 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libssh2 1.10.0 ha35d2d1_2 conda-forge
libstdcxx-ng 12.1.0 ha89aaad_16 conda-forge
libtiff 4.3.0 h542a066_3 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp 1.2.2 h3452ae3_0 conda-forge
libwebp-base 1.2.2 h7f98852_1 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libzip 1.8.0 h1c5bbd1_1 conda-forge
libzlib 1.2.11 h166bdaf_1014 conda-forge
llvmlite 0.39.0 pypi_0 pypi
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
lzo 2.10 h516909a_1000 conda-forge
markupsafe 2.1.1 py39hb9d737c_1 conda-forge
matplotlib-base 3.4.3 py39h2fa2bec_2 conda-forge
matplotlib-inline 0.1.3 pyhd8ed1ab_0 conda-forge
mbuild 0.15.1 pyhd8ed1ab_0 conda-forge
mdanalysis 2.2.0 py39h1832856_0 conda-forge
mdanalysistests 2.2.0 pyhd8ed1ab_1 conda-forge
mdtraj 1.9.7 py39h138c130_1 conda-forge
mistune 0.8.4 py39h3811e60_1005 conda-forge
mmpbsa-py 16.0 pypi_0 pypi
mmtf-python 1.1.3 pyhd8ed1ab_0 conda-forge
monty 2022.4.26 pypi_0 pypi
mpmath 1.2.1 pypi_0 pypi
mrcfile 1.4.2 pyhd8ed1ab_0 conda-forge
msgpack-python 1.0.4 py39hf939315_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
natsort 8.1.0 pypi_0 pypi
nb_conda 2.2.1 unix_6 conda-forge
nb_conda_kernels 2.3.1 py39hf3d152e_1 conda-forge
nbclassic 0.3.7 pypi_0 pypi
nbclient 0.6.4 pyhd8ed1ab_1 conda-forge
nbconvert 6.5.0 pyhd8ed1ab_0 conda-forge
nbconvert-core 6.5.0 pyhd8ed1ab_0 conda-forge
nbconvert-pandoc 6.5.0 pyhd8ed1ab_0 conda-forge
nbformat 5.4.0 pyhd8ed1ab_0 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
nest-asyncio 1.5.5 pyhd8ed1ab_0 conda-forge
netcdf-fortran 4.5.4 nompi_h2b6e579_100 conda-forge
netcdf4 1.6.0 nompi_py39hf5a3a3f_100 conda-forge
networkx 2.8.3 pyhd8ed1ab_0 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
notebook 6.4.12 pyha770c72_0 conda-forge
notebook-shim 0.1.0 pypi_0 pypi
numba 0.56.0 pypi_0 pypi
numexpr 2.8.0 py39h194a79d_102 conda-forge
numpy 1.22.4 py39hc58783e_0 conda-forge
ocl-icd 2.3.1 h7f98852_0 conda-forge
ocl-icd-system 1.0.0 1 conda-forge
openeye-toolkits 2021.2.0 py39_0 openeye
openff-forcefields 2.0.0 pyh6c4a22f_0 conda-forge
openff-interchange 0.1.4 pyhd8ed1ab_0 conda-forge
openff-interchange-base 0.1.4 pyh6c4a22f_0 conda-forge
openff-toolkit 0.10.6+4.g97462b88.dirty dev_0 <develop>
openff-toolkit-base 0.10.6 pyhd8ed1ab_0 conda-forge
openff-units 0.1.6 pyh6c4a22f_0 conda-forge
openff-utilities 0.1.5 pyh6c4a22f_0 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openmm 7.7.0 py39h15fbce5_1 conda-forge
openssl 3.0.5 h166bdaf_2 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
packmol 20.010 h86c2bf4_0 conda-forge
packmol-memgen 1.2.1rc0 pypi_0 pypi
palettable 3.3.0 pypi_0 pypi
pandas 1.4.2 py39h1832856_1 conda-forge
pandoc 2.18 ha770c72_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
panedr 0.5.2 py_0 conda-forge
parmed 3.4.3 py39h5a03fae_2 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
patsy 0.5.2 pyhd8ed1ab_0 conda-forge
pbr 5.9.0 pyhd8ed1ab_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pdb4amber 20.1 pypi_0 pypi
perl 5.32.1 2_h7f98852_perl5 conda-forge
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
physical_validation 1.0.4 pyhd8ed1ab_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 9.1.1 py39hae2aec6_0 conda-forge
pint 0.19.2 pyhd8ed1ab_0 conda-forge
pip 22.1.1 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
plotly 5.10.0 pypi_0 pypi
pluggy 1.0.0 py39hf3d152e_3 conda-forge
prometheus_client 0.14.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.29 pyha770c72_0 conda-forge
protobuf 3.20.1 py39h5a03fae_0 conda-forge
psutil 5.9.1 py39hb9d737c_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
py 1.11.0 pyh6c4a22f_0 conda-forge
py3dmol 1.8.1 pypi_0 pypi
pybtex 0.24.0 pypi_0 pypi
pycairo 1.21.0 py39h0934665_1 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pydantic 1.9.1 py39hb9d737c_0 conda-forge
pygments 2.12.0 pyhd8ed1ab_0 conda-forge
pymatgen 2022.8.23 pypi_0 pypi
pymbar 3.0.7 py39hd257fcd_0 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
pyrsistent 0.18.1 py39hb9d737c_1 conda-forge
pytables 3.7.0 py39h2669a42_0 conda-forge
pytest 7.1.2 py39hf3d152e_0 conda-forge
python 3.9.12 h2660328_1_cpython conda-forge
python-constraint 1.4.0 py_0 conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.15.3 pyhd8ed1ab_0 conda-forge
python_abi 3.9 2_cp39 conda-forge
pytraj 2.0.6 pypi_0 pypi
pytz 2022.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0 pypi_0 pypi
pyzmq 23.1.0 py39headdf64_0 conda-forge
rdkit 2022.03.3 py39h89e00b9_0 conda-forge
readline 8.1 h46c0cb4_0 conda-forge
remd-analysis 0+untagged.30.g5d9ec46 dev_0 <develop>
reportlab 3.5.68 py39he59360d_1 conda-forge
requests 2.28.0 pypi_0 pypi
ruamel-yaml 0.17.21 pypi_0 pypi
ruamel-yaml-clib 0.2.6 pypi_0 pypi
sander 16.0 pypi_0 pypi
scikit-learn 1.1.1 py39h4037b75_0 conda-forge
scipy 1.8.1 py39he49c0e8_0 conda-forge
seaborn 0.11.2 hd8ed1ab_0 conda-forge
seaborn-base 0.11.2 pyhd8ed1ab_0 conda-forge
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setuptools 62.3.2 py39hf3d152e_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
smirnoff99frosst 1.1.0 pyh44b312d_0 conda-forge
snappy 1.1.9 hbd366e4_1 conda-forge
sniffio 1.2.0 pypi_0 pypi
sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.3.2.post1 pypi_0 pypi
spglib 2.0.0 pypi_0 pypi
sqlalchemy 1.4.37 py39hb9d737c_0 conda-forge
sqlite 3.38.5 h4ff8645_0 conda-forge
stack_data 0.2.0 pyhd8ed1ab_0 conda-forge
statsmodels 0.13.2 py39hce5d2b2_0 conda-forge
sympy 1.11.1 pypi_0 pypi
tabulate 0.8.10 pypi_0 pypi
tenacity 8.0.1 pypi_0 pypi
terminado 0.15.0 py39hf3d152e_0 conda-forge
threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge
tidynamics 1.0.0 py_0 conda-forge
tinycss2 1.1.1 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tornado 6.1 py39hb9d737c_3 conda-forge
tqdm 4.64.0 pyhd8ed1ab_0 conda-forge
traitlets 5.2.2.post1 pyhd8ed1ab_0 conda-forge
typing-extensions 4.2.0 hd8ed1ab_1 conda-forge
typing_extensions 4.2.0 pyha770c72_1 conda-forge
tzdata 2022a h191b570_0 conda-forge
uncertainties 3.1.7 pypi_0 pypi
urllib3 1.26.9 pypi_0 pypi
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 pypi_0 pypi
websocket-client 1.3.2 pypi_0 pypi
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxt 1.2.1 h7f98852_2 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zeromq 4.3.4 h9c3ff4c_1 conda-forge
zipp 3.8.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.11 h166bdaf_1014 conda-forge
zstd 1.5.2 h8a70e8d_1 conda-forge
Issue Analytics
- State:
- Created a year ago
- Comments:12 (7 by maintainers)
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For a system with 373 atoms, I ran the AmberTools AM1BCC partial charge assignment on my computer for around 18 hours and ended up canceling the job because it wouldn’t finish. On the old version (0.10.6) where I modified the OpenEyeToolkitWrapper object to perform AM1BCC on larger systems (up to 500 atoms), that seemed to take a couple of hours, rather than the 18+ hours seen with the AmberTools implementation.
Okay, I realize now why I had a later version of the toolkit installed. I installed the OpenFF toolkit from source so I could make some changes to the OpenEyeWrapper allowing it to be run for systems with up to 500 atoms. However I built this on the
masterbranch, not themainbranch, so when I installed using the setup.py file, I installed an older version of the toolkit. While the OpenEye AM1BCC implementation is slow, I think it’s still faster than the AmberTools implementation.