Converting output to other formats?

[qsabanes]

Description

I've been testing some of the examples in the documentation and so far so good, even with my molecules. What I'm trying to look is if I can convert the resulting outputs into AMBER and/or GROMACS format? I've seen that in the Supporting Info of Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale you mention the use of parmed when running the free energy tests. I've been trying to look both in this and parmed's documentation with no luck. I'd like to replicate the same test described there in similar conditions.

The test command I ran with my mol was the following:

openff-bespoke executor run --file             "m1.sdf" \
                            --workflow           "default"               \
                            --output             "m1.json"    \
                            --output-force-field "m1.offxml"  \
                            --n-qc-compute-workers 2                     \
                            --qc-compute-n-cores   1                     \
                            --default-qc-spec xtb gfn2xtb none

Software versions

• Which operating system and version are you using? Ubuntu 22.04.2 LTS
• How did you install BespokeFit? As per documentation:

conda create -n bespokefit -y -c conda-forge mamba python=3.9
conda activate bespokefit 
mamba install -y -c conda-forge openff-bespokefit xtb-python ambertools

• Are you using Apple Silicon? If so, are you running BespokeFit in Rosetta or directly? No Apple Silicon. Running directly
• What is the output of running conda list?

Output of conda list

_libgcc_mutex             0.1                 conda_forge    conda-forge

_openmp_mutex             4.5                       2_gnu    conda-forge

ambertools                23.0             py39h4856ba4_1    conda-forge

amberutils                21.0                     pypi_0    pypi

amqp                      5.1.1              pyhd8ed1ab_0    conda-forge

anyio                     3.7.0              pyhd8ed1ab_1    conda-forge

argcomplete               3.1.1              pyhd8ed1ab_0    conda-forge

argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge

argon2-cffi-bindings      21.2.0           py39hb9d737c_3    conda-forge

arpack                    3.7.0                hdefa2d7_2    conda-forge

asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge

astunparse                1.6.3              pyhd8ed1ab_0    conda-forge

async-timeout             4.0.2              pyhd8ed1ab_0    conda-forge

attrs                     23.1.0             pyh71513ae_1    conda-forge

aws-c-auth                0.6.28               h9536e0a_4    conda-forge

aws-c-cal                 0.5.27               hf85dbcb_0    conda-forge

aws-c-common              0.8.20               hd590300_0    conda-forge

aws-c-compression         0.2.17               h4b87b72_0    conda-forge

aws-c-event-stream        0.3.0                h6a13d8e_5    conda-forge

aws-c-http                0.7.8                hf549d3b_3    conda-forge

aws-c-io                  0.13.24              h0d05201_1    conda-forge

aws-c-mqtt                0.8.13               h39123d0_1    conda-forge

aws-c-s3                  0.3.4                h0c75bb1_4    conda-forge

aws-c-sdkutils            0.1.10               h4b87b72_0    conda-forge

aws-checksums             0.1.16               h4b87b72_0    conda-forge

aws-crt-cpp               0.20.2               hf0dd499_8    conda-forge

aws-sdk-cpp               1.10.57             h8101662_14    conda-forge

backcall                  0.2.0              pyh9f0ad1d_0    conda-forge

backports                 1.0                pyhd8ed1ab_3    conda-forge

backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge

basis_set_exchange        0.9.1              pyhd8ed1ab_0    conda-forge

beautifulsoup4            4.12.2             pyha770c72_0    conda-forge

billiard                  3.6.4.0          py39hb9d737c_3    conda-forge

bleach                    6.0.0              pyhd8ed1ab_0    conda-forge

blosc                     1.21.4               h0f2a231_0    conda-forge

boltons                   23.0.0             pyhd8ed1ab_0    conda-forge

boost                     1.78.0           py39h7c9e3ff_4    conda-forge

boost-cpp                 1.78.0               h6582d0a_3    conda-forge

brotli                    1.0.9                h166bdaf_8    conda-forge

brotli-bin                1.0.9                h166bdaf_8    conda-forge

bzip2                     1.0.8                h7f98852_4    conda-forge

c-ares                    1.19.1               hd590300_0    conda-forge

c-blosc2                  2.9.2                hb4ffafa_0    conda-forge

ca-certificates           2023.5.7             hbcca054_0    conda-forge

cached-property           1.5.2                hd8ed1ab_1    conda-forge

cached_property           1.5.2              pyha770c72_1    conda-forge

cachetools                5.3.0              pyhd8ed1ab_0    conda-forge

cairo                     1.16.0            hbbf8b49_1016    conda-forge

celery                    5.2.7              pyhd8ed1ab_0    conda-forge

certifi                   2023.5.7           pyhd8ed1ab_0    conda-forge

cffi                      1.15.1           py39he91dace_3    conda-forge

charset-normalizer        3.1.0              pyhd8ed1ab_0    conda-forge

chemper                   1.0.1              pyhd8ed1ab_0    conda-forge

click                     8.1.3           unix_pyhd8ed1ab_2    conda-forge

click-didyoumean          0.3.0              pyhd8ed1ab_0    conda-forge

click-option-group        0.5.6              pyhd8ed1ab_0    conda-forge

click-plugins             1.1.1                      py_0    conda-forge

click-repl                0.2.0              pyhd8ed1ab_0    conda-forge

colorama                  0.4.6              pyhd8ed1ab_0    conda-forge

comm                      0.1.3              pyhd8ed1ab_0    conda-forge

conda                     23.3.1           py39hf3d152e_0    conda-forge

conda-package-handling    2.0.2              pyh38be061_0    conda-forge

conda-package-streaming   0.8.0              pyhd8ed1ab_0    conda-forge

contourpy                 1.0.7            py39h4b4f3f3_0    conda-forge

cryptography              41.0.1           py39hd4f0224_0    conda-forge

cudatoolkit               11.8.0              h37601d7_11    conda-forge

curl                      8.1.2                h409715c_0    conda-forge

cycler                    0.11.0             pyhd8ed1ab_0    conda-forge

cython                    0.29.35          py39h3d6467e_0    conda-forge

debugpy                   1.6.7            py39h227be39_0    conda-forge

decorator                 5.1.1              pyhd8ed1ab_0    conda-forge

defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge

edgembar                  0.2                      pypi_0    pypi

entrypoints               0.4                pyhd8ed1ab_0    conda-forge

exceptiongroup            1.1.1              pyhd8ed1ab_0    conda-forge

executing                 1.2.0              pyhd8ed1ab_0    conda-forge

expat                     2.5.0                hcb278e6_1    conda-forge

fastapi                   0.86.0             pyhd8ed1ab_0    conda-forge

fftw                      3.3.10          nompi_hc118613_108    conda-forge

flit-core                 3.9.0              pyhd8ed1ab_0    conda-forge

fmt                       9.1.0                h924138e_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                2.14.2               h14ed4e7_0    conda-forge

fonts-conda-ecosystem     1                             0    conda-forge

fonts-conda-forge         1                             0    conda-forge

fonttools                 4.40.0           py39hd1e30aa_0    conda-forge

forcebalance              1.9.5            py39h0354152_0    conda-forge

freetype                  2.12.1               hca18f0e_1    conda-forge

future                    0.18.3             pyhd8ed1ab_0    conda-forge

geometric                 1.0                pyhd8ed1ab_1    conda-forge

gettext                   0.21.1               h27087fc_0    conda-forge

gflags                    2.2.2             he1b5a44_1004    conda-forge

glog                      0.6.0                h6f12383_0    conda-forge

greenlet                  2.0.2            py39h3d6467e_1    conda-forge

h11                       0.14.0             pyhd8ed1ab_0    conda-forge

h2                        4.1.0              pyhd8ed1ab_0    conda-forge

h5py                      3.8.0           nompi_py39h89bf01e_101    conda-forge

hdf4                      4.2.15               h501b40f_6    conda-forge

hdf5                      1.14.0          nompi_hb72d44e_103    conda-forge

hpack                     4.0.0              pyh9f0ad1d_0    conda-forge

httpcore                  0.17.2             pyhd8ed1ab_0    conda-forge

httpx                     0.24.1             pyhd8ed1ab_0    conda-forge

hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge

icu                       72.1                 hcb278e6_0    conda-forge

idna                      3.4                pyhd8ed1ab_0    conda-forge

importlib-metadata        6.6.0              pyha770c72_0    conda-forge

importlib-resources       5.12.0             pyhd8ed1ab_0    conda-forge

importlib_metadata        6.6.0                hd8ed1ab_0    conda-forge

importlib_resources       5.12.0             pyhd8ed1ab_0    conda-forge

ipykernel                 6.23.1             pyh210e3f2_0    conda-forge

ipython                   8.14.0             pyh41d4057_0    conda-forge

ipython_genutils          0.2.0                      py_1    conda-forge

ipywidgets                7.7.5              pyhd8ed1ab_0    conda-forge

jedi                      0.18.2             pyhd8ed1ab_0    conda-forge

jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge

joblib                    1.2.0              pyhd8ed1ab_0    conda-forge

jsonpatch                 1.32               pyhd8ed1ab_0    conda-forge

jsonpointer               2.0                        py_0    conda-forge

jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge

jupyter_client            8.2.0              pyhd8ed1ab_0    conda-forge

jupyter_core              5.3.0            py39hf3d152e_0    conda-forge

jupyter_events            0.6.3              pyhd8ed1ab_0    conda-forge

jupyter_server            2.6.0              pyhd8ed1ab_0    conda-forge

jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge

jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge

jupyterlab_widgets        1.1.4              pyhd8ed1ab_0    conda-forge

keyutils                  1.6.1                h166bdaf_0    conda-forge

kiwisolver                1.4.4            py39hf939315_1    conda-forge

kombu                     5.2.4            py39hf3d152e_2    conda-forge

krb5                      1.20.1               h81ceb04_0    conda-forge

lcms2                     2.15                 haa2dc70_1    conda-forge

ld_impl_linux-64          2.40                 h41732ed_0    conda-forge

lerc                      4.0.0                h27087fc_0    conda-forge

libabseil                 20230125.2      cxx17_h59595ed_2    conda-forge

libaec                    1.0.6                hcb278e6_1    conda-forge

libarchive                3.6.2                h039dbb9_1    conda-forge

libarrow                  12.0.0           hed73b3e_7_cpu    conda-forge

libblas                   3.9.0           17_linux64_openblas    conda-forge

libbrotlicommon           1.0.9                h166bdaf_8    conda-forge

libbrotlidec              1.0.9                h166bdaf_8    conda-forge

libbrotlienc              1.0.9                h166bdaf_8    conda-forge

libcblas                  3.9.0           17_linux64_openblas    conda-forge

libcrc32c                 1.1.2                h9c3ff4c_0    conda-forge

libcurl                   8.1.2                h409715c_0    conda-forge

libdeflate                1.18                 h0b41bf4_0    conda-forge

libedit                   3.1.20191231         he28a2e2_2    conda-forge

libev                     4.33                 h516909a_1    conda-forge

libevent                  2.1.12               hf998b51_1    conda-forge

libexpat                  2.5.0                hcb278e6_1    conda-forge

libffi                    3.4.2                h7f98852_5    conda-forge

libgcc-ng                 13.1.0               he5830b7_0    conda-forge

libgfortran-ng            13.1.0               h69a702a_0    conda-forge

libgfortran5              13.1.0               h15d22d2_0    conda-forge

libglib                   2.76.3               hebfc3b9_0    conda-forge

libgomp                   13.1.0               he5830b7_0    conda-forge

libgoogle-cloud           2.11.0               hac9eb74_1    conda-forge

libgrpc                   1.54.2               hb20ce57_2    conda-forge

libiconv                  1.17                 h166bdaf_0    conda-forge

libjpeg-turbo             2.1.5.1              h0b41bf4_0    conda-forge

liblapack                 3.9.0           17_linux64_openblas    conda-forge

libmamba                  1.4.2                hcea66bb_0    conda-forge

libmambapy                1.4.2            py39hf0aba66_0    conda-forge

libnetcdf                 4.9.2           nompi_h0f3d0bb_105    conda-forge

libnghttp2                1.52.0               h61bc06f_0    conda-forge

libnsl                    2.0.0                h7f98852_0    conda-forge

libnuma                   2.0.16               h0b41bf4_1    conda-forge

libopenblas               0.3.23          pthreads_h80387f5_0    conda-forge

libpng                    1.6.39               h753d276_0    conda-forge

libprotobuf               3.21.12              h3eb15da_0    conda-forge

libsodium                 1.0.18               h36c2ea0_1    conda-forge

libsolv                   0.7.24               h3eb15da_0    conda-forge

libsqlite                 3.42.0               h2797004_0    conda-forge

libssh2                   1.11.0               h0841786_0    conda-forge

libstdcxx-ng              13.1.0               hfd8a6a1_0    conda-forge

libthrift                 0.18.1               h8fd135c_2    conda-forge

libtiff                   4.5.0                ha587672_6    conda-forge

libutf8proc               2.8.0                h166bdaf_0    conda-forge

libuuid                   2.38.1               h0b41bf4_0    conda-forge

libwebp-base              1.3.0                h0b41bf4_0    conda-forge

libxcb                    1.15                 h0b41bf4_0    conda-forge

libxml2                   2.11.4               h0d562d8_0    conda-forge

libxslt                   1.1.37               h0054252_1    conda-forge

libzip                    1.9.2                hc929e4a_1    conda-forge

libzlib                   1.2.13               hd590300_5    conda-forge

lxml                      4.9.1            py39hb9d737c_0    conda-forge

lz4-c                     1.9.4                hcb278e6_0    conda-forge

lzo                       2.10              h516909a_1000    conda-forge

mamba                     1.4.2            py39hc5d2bb1_0    conda-forge

markdown-it-py            3.0.0              pyhd8ed1ab_0    conda-forge

markupsafe                2.1.3            py39hd1e30aa_0    conda-forge

matplotlib-base           3.7.1            py39he190548_0    conda-forge

matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge

mctc-lib                  0.3.1                h74f4db8_0    conda-forge

mdtraj                    1.9.7            py39h62423bb_4    conda-forge

mdurl                     0.1.0              pyhd8ed1ab_0    conda-forge

mistune                   2.0.5              pyhd8ed1ab_0    conda-forge

mmpbsa-py                 16.0                     pypi_0    pypi

msgpack-python            1.0.5            py39h4b4f3f3_0    conda-forge

munkres                   1.1.4              pyh9f0ad1d_0    conda-forge

nbclassic                 1.0.0              pyhb4ecaf3_1    conda-forge

nbclient                  0.8.0              pyhd8ed1ab_0    conda-forge

nbconvert                 7.4.0              pyhd8ed1ab_0    conda-forge

nbconvert-core            7.4.0              pyhd8ed1ab_0    conda-forge

nbconvert-pandoc          7.4.0              pyhd8ed1ab_0    conda-forge

nbformat                  5.9.0              pyhd8ed1ab_0    conda-forge

ncurses                   6.4                  hcb278e6_0    conda-forge

nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge

netcdf-fortran            4.6.1           nompi_h4f3791c_100    conda-forge

networkx                  3.1                pyhd8ed1ab_0    conda-forge

nglview                   3.0.5              pyhe68d6a8_0    conda-forge

nomkl                     1.0                  h5ca1d4c_0    conda-forge

notebook                  6.5.4              pyha770c72_0    conda-forge

notebook-shim             0.2.3              pyhd8ed1ab_0    conda-forge

numexpr                   2.8.4           py39h5ef5dce_100    conda-forge

numpy                     1.24.3           py39h6183b62_0    conda-forge

ocl-icd                   2.3.1                h7f98852_0    conda-forge

ocl-icd-system            1.0.0                         1    conda-forge

openff-amber-ff-ports     0.0.3              pyh6c4a22f_0    conda-forge

openff-bespokefit         0.2.2              pyhd8ed1ab_0    conda-forge

openff-forcefields        2023.05.1          pyh1a96a4e_1    conda-forge

openff-fragmenter-base    0.2.0              pyhd8ed1ab_0    conda-forge

openff-interchange        0.3.4              pyhd8ed1ab_2    conda-forge

openff-interchange-base   0.3.4              pyhd8ed1ab_2    conda-forge

openff-models             0.0.5              pyh1a96a4e_0    conda-forge

openff-qcsubmit           0.4.1              pyhd8ed1ab_0    conda-forge

openff-toolkit            0.13.1             pyhd8ed1ab_0    conda-forge

openff-toolkit-base       0.13.1             pyhd8ed1ab_0    conda-forge

openff-units              0.2.0              pyh1a96a4e_2    conda-forge

openff-utilities          0.1.8              pyh1a96a4e_0    conda-forge

openjpeg                  2.5.0                hfec8fc6_2    conda-forge

openmm                    8.0.0            py39h7d85326_1    conda-forge

openssl                   3.1.1                hd590300_1    conda-forge

orc                       1.8.3                h2f23424_1    conda-forge

overrides                 7.3.1              pyhd8ed1ab_0    conda-forge

packaging                 23.1               pyhd8ed1ab_0    conda-forge

packmol                   20.010               h86c2bf4_0    conda-forge

packmol-memgen            2023.2.24                pypi_0    pypi

pandas                    2.0.2            py39h40cae4c_0    conda-forge

pandoc                    2.19.2               h32600fe_2    conda-forge

pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge

panedr                    0.7.1              pyhd8ed1ab_0    conda-forge

parmed                    4.1.0            py39h227be39_0    conda-forge

parso                     0.8.3              pyhd8ed1ab_0    conda-forge

pbr                       5.11.1             pyhd8ed1ab_0    conda-forge

pcre2                     10.40                hc3806b6_0    conda-forge

pdb4amber                 22.0                     pypi_0    pypi

perl                      5.32.1          2_h7f98852_perl5    conda-forge

pexpect                   4.8.0              pyh1a96a4e_2    conda-forge

pickleshare               0.7.5                   py_1003    conda-forge

pillow                    9.5.0            py39haaeba84_1    conda-forge

pint                      0.21               pyhd8ed1ab_0    conda-forge

pip                       23.1.2             pyhd8ed1ab_0    conda-forge

pixman                    0.40.0               h36c2ea0_0    conda-forge

pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge

platformdirs              3.5.3              pyhd8ed1ab_0    conda-forge

plotly                    5.15.0             pyhd8ed1ab_0    conda-forge

pluggy                    1.0.0              pyhd8ed1ab_5    conda-forge

pooch                     1.7.0              pyha770c72_3    conda-forge

prometheus_client         0.17.0             pyhd8ed1ab_0    conda-forge

prompt-toolkit            3.0.38             pyha770c72_0    conda-forge

prompt_toolkit            3.0.38               hd8ed1ab_0    conda-forge

psutil                    5.9.5            py39h72bdee0_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-cpuinfo                9.0.0              pyhd8ed1ab_0    conda-forge

pyarrow                   12.0.0          py39he4327e9_7_cpu    conda-forge

pybind11-abi              4                    hd8ed1ab_3    conda-forge

pycairo                   1.23.0           py39h23c5bb2_0    conda-forge

pycosat                   0.6.4            py39hb9d737c_1    conda-forge

pycparser                 2.21               pyhd8ed1ab_0    conda-forge

pydantic                  1.10.9           py39hd1e30aa_0    conda-forge

pyedr                     0.7.1              pyhd8ed1ab_0    conda-forge

pygments                  2.15.1             pyhd8ed1ab_0    conda-forge

pymbar                    3.1.1            py39h2ae25f5_2    conda-forge

pymsmt                    22.0                     pypi_0    pypi

pyopenssl                 23.2.0             pyhd8ed1ab_1    conda-forge

pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge

pyrsistent                0.19.3           py39h72bdee0_0    conda-forge

pysocks                   1.7.1              pyha2e5f31_6    conda-forge

pytables                  3.8.0            py39hac3db9e_1    conda-forge

python                    3.9.16          h2782a2a_0_cpython    conda-forge

python-constraint         1.4.0                      py_0    conda-forge

python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge

python-fastjsonschema     2.17.1             pyhd8ed1ab_0    conda-forge

python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge

python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge

python_abi                3.9                      3_cp39    conda-forge

pytraj                    2.0.6                    pypi_0    pypi

pytz                      2023.3             pyhd8ed1ab_0    conda-forge

pyyaml                    6.0              py39hb9d737c_5    conda-forge

pyzmq                     25.1.0           py39hb257651_0    conda-forge

qcelemental               0.25.1             pyhd8ed1ab_1    conda-forge

qcengine                  0.26.0             pyhd8ed1ab_0    conda-forge

qcportal                  0.15.8             pyhd8ed1ab_0    conda-forge

rdkit                     2023.03.1        py39h55a5abb_0    conda-forge

rdma-core                 28.9                 h59595ed_1    conda-forge

re2                       2023.03.02           h8c504da_0    conda-forge

readline                  8.2                  h8228510_1    conda-forge

redis-py                  4.5.5              pyhd8ed1ab_0    conda-forge

redis-server              7.0.11               h3358134_0    conda-forge

regex                     2023.6.3         py39hd1e30aa_0    conda-forge

reportlab                 3.6.13           py39h12ba270_0    conda-forge

reproc                    14.2.4               h0b41bf4_0    conda-forge

reproc-cpp                14.2.4               hcb278e6_0    conda-forge

requests                  2.31.0             pyhd8ed1ab_0    conda-forge

rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge

rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge

rich                      13.4.2             pyhd8ed1ab_0    conda-forge

ruamel.yaml               0.17.31          py39hd1e30aa_0    conda-forge

ruamel.yaml.clib          0.2.7            py39h72bdee0_1    conda-forge

s2n                       1.3.45               h06160fa_0    conda-forge

sander                    22.0                     pypi_0    pypi

scipy                     1.10.1           py39h6183b62_3    conda-forge

send2trash                1.8.2              pyh41d4057_0    conda-forge

setuptools                67.7.2             pyhd8ed1ab_0    conda-forge

six                       1.16.0             pyh6c4a22f_0    conda-forge

smirnoff99frosst          1.1.0              pyh44b312d_0    conda-forge

snappy                    1.1.10               h9fff704_0    conda-forge

sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge

soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge

sqlalchemy                2.0.16           py39hd1e30aa_0    conda-forge

stack_data                0.6.2              pyhd8ed1ab_0    conda-forge

starlette                 0.20.4             pyhd8ed1ab_1    conda-forge

tenacity                  8.2.2              pyhd8ed1ab_0    conda-forge

terminado                 0.17.1             pyh41d4057_0    conda-forge

tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge

tk                        8.6.12               h27826a3_0    conda-forge

toolz                     0.12.0             pyhd8ed1ab_0    conda-forge

tornado                   6.3.2            py39hd1e30aa_0    conda-forge

torsiondrive              1.1.0              pyhd8ed1ab_0    conda-forge

tqdm                      4.65.0             pyhd8ed1ab_1    conda-forge

traitlets                 5.9.0              pyhd8ed1ab_0    conda-forge

typing-extensions         4.6.3                hd8ed1ab_0    conda-forge

typing_extensions         4.6.3              pyha770c72_0    conda-forge

typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge

tzdata                    2023c                h71feb2d_0    conda-forge

ucx                       1.14.1               hf587318_2    conda-forge

unicodedata2              15.0.0           py39hb9d737c_0    conda-forge

unidecode                 1.3.6              pyhd8ed1ab_0    conda-forge

urllib3                   2.0.3              pyhd8ed1ab_0    conda-forge

uvicorn                   0.22.0           py39hf3d152e_0    conda-forge

vine                      5.0.0              pyhd8ed1ab_1    conda-forge

wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge

webencodings              0.5.1                      py_1    conda-forge

websocket-client          1.5.3              pyhd8ed1ab_0    conda-forge

wheel                     0.40.0             pyhd8ed1ab_0    conda-forge

widgetsnbextension        3.6.4              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               1.8.5                h8ee46fc_0    conda-forge

xorg-libxau               1.0.11               hd590300_0    conda-forge

xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge

xorg-libxext              1.3.4                h0b41bf4_2    conda-forge

xorg-libxrender           0.9.10            h7f98852_1003    conda-forge

xorg-libxt                1.3.0                hd590300_0    conda-forge

xorg-renderproto          0.11.1            h7f98852_1002    conda-forge

xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge

xorg-xproto               7.0.31            h7f98852_1007    conda-forge

xtb                       6.5.1                h03160e7_1    conda-forge

xtb-python                22.1             py39h72bdee0_0    conda-forge

xz                        5.2.6                h166bdaf_0    conda-forge

yaml                      0.2.5                h7f98852_2    conda-forge

yaml-cpp                  0.7.0                h27087fc_2    conda-forge

zeromq                    4.3.4                h9c3ff4c_1    conda-forge

zipp                      3.15.0             pyhd8ed1ab_0    conda-forge

zlib                      1.2.13               hd590300_5    conda-forge

zlib-ng                   2.0.7                h0b41bf4_0    conda-forge

zstandard                 0.19.0           py39h29414ee_1    conda-forge

zstd                      1.5.2                h3eb15da_6    conda-forge

Many thanks!

[Yoshanuikabundi]

Hey! Interchange is our tool for this. If you take that m1.offxml and pass it to Interchange.from_smirnoff() along with the molecule you parametrized you'll get an object that can be converted to a parametrized Amber, GROMACS or OpenMM simulation system. You can also set up a whole topology with positions and box vectors and solvent and so on, parametrize it with the OFFXML, and then export it to those software packages. There's some information on how it all fits together here.

Unfortunately we don't have an easy way to produce, say, .ITP files for single molecules (or whatever the Amber equivalent is) - but hopefully between the Toolkit and Interchange you can do everything you needed!

Hope this helps!

[mattwthompson]

(Looks like I goofed and added a 👎 react yesterday - sorry about that!)

[qsabanes]

Thanks for this!
I managed an .frcmod for my molecule so I think I should be good to go. I'll comment later because I need at least a couple ligands to test but I wanted to say thanks beforehand! :)