Question about ABFE using restraint search
Closed this issue · 13 comments
Hi,
I went through the tutorial in notebook for website, and everything is good. But when I download BioSimSpace, and ran in my local pc.
For the ABFE tutorial (04_fep/03_ABFE), it does not have "RestraintSearch" attribute in BioSimSpace.FreeEnergy.
It seems that this feature is not available anymore. If I want to search Restraints for Absolute binding free energy, how can I do that?
Thank you !
Hello there. The ABFE implementation is currently part of the Exscientia sandpit, so you'll need to use import BioSimSpace.Sandpit.Exscientia as BSS. This is mentioned in the tutorial here. Apologies if it wasn't clear.
Thank you so much for your quick reply! It is my fault I did not read it clearly. I am sorry.
Just out of curiosity, does BSS support replica exchange in ABFE or RBFE?
Not at present. This is something that we plan to work on in the near future.
Hi @lohedges,
I found a issue. I used my system and tried to run the RestraintSearch.analyse, but it failed. I found out that the reason for the failure is that I load the gromacs topology rather than amber topology file. After I converted to amber topology file(prm7), then it can run.
This is the error message it showed:
And here is my code:
import BioSimSpace.Sandpit.Exscientia as BSS
import pandas as pd
gro="output_setup/ejm31/com/05_npt_relax/05_npt_relax_out.gro"
top="output_setup/ejm31/com/05_npt_relax/05_npt_relax.top"
system=BSS.IO.readMolecules([gro,top])
lig = BSS.Align.decouple(system[0])
system.updateMolecule(0, lig)
protocol = BSS.Protocol.Production(runtime=0.01*BSS.Units.Time.nanosecond)
restraint_search = BSS.FreeEnergy.RestraintSearch(system, protocol=protocol, engine='gromacs', work_dir='restraint_search')
restraint_search.start()
restraint_search.wait()
restraint = restraint_search.analyse(method='BSS', block=True)
I just want to report this issue.
Thank you!
That's strange. I didn't write this part of the code so will ask @fjclark to comment when he's back. Ideally this should be interoperable and not dependent on specific naming of the topology file, which looks to be the problem here. I've checked the latest version of the code and the selection string appears to be identical. (Although there aren't the commented print statements, but maybe these are yours from debugging.)
05_npt_relax.zip
Here is the files I used for the system. In case you need it.
Thanks!
Many thanks, this will be really helpful.
Hi @jnutyj, thanks for reporting and for providing the files.
I've tried to reproduce this locally using your script and the files provided, but it works fine for me. It looks like your issue is that MDAnalysis is failing to read the trajectory and topology, which causes the MDAnalysis universe object (u) to be None. Could you let us know the versions of GROMACS and MDAnalysis that you're using, please? I'm using MDAnalysis 2.7.0 and I've tried both GROMACS 22.2 and 23.1. Could you please share the output of conda list?
It would be good if the error message was more helpful - do you think the BSS warning about MDAnalysis failing to read the trajectory should be an exception instead @lohedges?
Thanks!
Hi @fjclark,
Here is my conda list
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
adjusttext 1.2.0 pyhd8ed1ab_0 conda-forge
alchemlyb 2.3.1 pyhd8ed1ab_0 conda-forge
alsa-lib 1.2.12 h4ab18f5_0 conda-forge
ambertools 23.6 cuda_None_nompi_py312h41aabf6_105 conda-forge
amberutils 21.0 pypi_0 pypi
annotated-types 0.7.0 pyhd8ed1ab_0 conda-forge
anyio 4.4.0 pyhd8ed1ab_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py312h98912ed_4 conda-forge
arpack 3.9.1 nompi_h77f6705_101 conda-forge
arrow 1.3.0 pyhd8ed1ab_0 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
astunparse 1.6.3 pyhd8ed1ab_0 conda-forge
async-lru 2.0.4 pyhd8ed1ab_0 conda-forge
atk-1.0 2.38.0 h04ea711_2 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
attrs 23.2.0 pyh71513ae_0 conda-forge
aws-c-auth 0.7.22 hbd3ac97_10 conda-forge
aws-c-cal 0.7.1 h87b94db_1 conda-forge
aws-c-common 0.9.23 h4ab18f5_0 conda-forge
aws-c-compression 0.2.18 he027950_7 conda-forge
aws-c-event-stream 0.4.2 h7671281_15 conda-forge
aws-c-http 0.8.2 he17ee6b_6 conda-forge
aws-c-io 0.14.10 h826b7d6_1 conda-forge
aws-c-mqtt 0.10.4 hcd6a914_8 conda-forge
aws-c-s3 0.6.0 h365ddd8_2 conda-forge
aws-c-sdkutils 0.1.16 he027950_3 conda-forge
aws-checksums 0.1.18 he027950_7 conda-forge
aws-crt-cpp 0.27.3 hda66527_2 conda-forge
aws-sdk-cpp 1.11.329 h46c3b66_9 conda-forge
azure-core-cpp 1.13.0 h935415a_0 conda-forge
azure-identity-cpp 1.8.0 hd126650_2 conda-forge
azure-storage-blobs-cpp 12.12.0 hd2e3451_0 conda-forge
azure-storage-common-cpp 12.7.0 h10ac4d7_1 conda-forge
azure-storage-files-datalake-cpp 12.11.0 h325d260_1 conda-forge
babel 2.14.0 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.3 pyha770c72_0 conda-forge
biopython 1.84 py312h9a8786e_0 conda-forge
biosimspace 2024.2.0 py312_0 openbiosim
bleach 6.1.0 pyhd8ed1ab_0 conda-forge
blosc 1.21.6 hef167b5_0 conda-forge
boost 1.84.0 h9cebb41_3 conda-forge
brotli 1.1.0 hd590300_1 conda-forge
brotli-bin 1.1.0 hd590300_1 conda-forge
brotli-python 1.1.0 py312h30efb56_1 conda-forge
bson 0.5.9 py_0 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.32.3 h4bc722e_0 conda-forge
c-blosc2 2.15.1 hc57e6cf_0 conda-forge
ca-certificates 2024.7.4 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.4.0 pyhd8ed1ab_0 conda-forge
cairo 1.18.0 hbb29018_2 conda-forge
certifi 2024.7.4 py312h06a4308_0
cffi 1.16.0 py312hf06ca03_0 conda-forge
cftime 1.6.4 py312h085067d_0 conda-forge
chardet 5.2.0 py312h7900ff3_1 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
cinnabar 0.4.1 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.2.2 pyhd8ed1ab_0 conda-forge
configargparse 1.7 pyhd8ed1ab_0 conda-forge
contourpy 1.2.1 py312h8572e83_0 conda-forge
coverage 7.6.0 py312h41a817b_0 conda-forge
cudatoolkit 11.8.0 h4ba93d1_13 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
debugpy 1.8.2 py312h7070661_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 1.2.2 pyhd8ed1ab_0 conda-forge
executing 2.0.1 pyhd8ed1ab_0 conda-forge
expat 2.6.2 h59595ed_0 conda-forge
fasteners 0.17.3 pyhd8ed1ab_0 conda-forge
fftw 3.3.10 nompi_hf1063bd_110 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 h77eed37_2 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 4.53.1 py312h41a817b_0 conda-forge
fqdn 1.5.1 pyhd8ed1ab_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gdk-pixbuf 2.42.12 hb9ae30d_0 conda-forge
gettext 0.22.5 h59595ed_2 conda-forge
gettext-tools 0.22.5 h59595ed_2 conda-forge
gflags 2.2.2 he1b5a44_1004 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
glib 2.80.3 h8a4344b_1 conda-forge
glib-tools 2.80.3 h73ef956_1 conda-forge
glog 0.7.1 hbabe93e_0 conda-forge
graphite2 1.3.13 h59595ed_1003 conda-forge
graphviz 11.0.0 hc68bbd7_0 conda-forge
greenlet 3.0.3 py312h30efb56_0 conda-forge
griddataformats 1.0.2 pyhd8ed1ab_0 conda-forge
gsd 3.3.0 py312h085067d_0 conda-forge
gsl 2.7 he838d99_0 conda-forge
gst-plugins-base 1.24.6 hbaaba92_0 conda-forge
gstreamer 1.24.6 haf2f30d_0 conda-forge
gtk2 2.24.33 h6470451_5 conda-forge
gts 0.7.6 h977cf35_4 conda-forge
gufe 1.0.0 pyhd8ed1ab_0 conda-forge
h11 0.14.0 pyhd8ed1ab_0 conda-forge
h2 4.1.0 pyhd8ed1ab_0 conda-forge
h5py 3.11.0 nompi_py312hb7ab980_102 conda-forge
harfbuzz 9.0.0 hfac3d4d_0 conda-forge
hdf4 4.2.15 h2a13503_7 conda-forge
hdf5 1.14.3 nompi_hdf9ad27_105 conda-forge
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
httpcore 1.0.5 pyhd8ed1ab_0 conda-forge
httpx 0.27.0 pyhd8ed1ab_0 conda-forge
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
icu 73.2 h59595ed_0 conda-forge
idna 3.7 pyhd8ed1ab_0 conda-forge
importlib-metadata 8.2.0 pyha770c72_0 conda-forge
importlib_metadata 8.2.0 hd8ed1ab_0 conda-forge
importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge
ipykernel 6.29.5 pyh3099207_0 conda-forge
ipython 8.26.0 pyh707e725_0 conda-forge
ipywidgets 8.1.3 pyhd8ed1ab_0 conda-forge
isoduration 20.11.0 pyhd8ed1ab_0 conda-forge
jax 0.4.31 pyhd8ed1ab_0 conda-forge
jaxlib 0.4.30 cpu_py312h17e8b90_0 conda-forge
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
joblib 1.4.2 pyhd8ed1ab_0 conda-forge
json5 0.9.25 pyhd8ed1ab_0 conda-forge
jsonpointer 3.0.0 py312h7900ff3_0 conda-forge
jsonschema 4.23.0 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge
jsonschema-with-format-nongpl 4.23.0 hd8ed1ab_0 conda-forge
jupyter-lsp 2.2.5 pyhd8ed1ab_0 conda-forge
jupyter_client 8.6.2 pyhd8ed1ab_0 conda-forge
jupyter_core 5.7.2 py312h7900ff3_0 conda-forge
jupyter_events 0.10.0 pyhd8ed1ab_0 conda-forge
jupyter_server 2.14.2 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.5.3 pyhd8ed1ab_0 conda-forge
jupyterlab 4.2.4 pyhd8ed1ab_0 conda-forge
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jupyterlab_server 2.27.3 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 3.0.11 pyhd8ed1ab_0 conda-forge
kcombu_bss 2023.29.01 h9bf148f_0 openbiosim
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.5 py312h8572e83_1 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lazy_import 0.2.2 pyhd8ed1ab_0 conda-forge
lcms2 2.16 hb7c19ff_0 conda-forge
ld_impl_linux-64 2.40 hf3520f5_7 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
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libarrow 17.0.0 h4b47046_3_cpu conda-forge
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libarrow-dataset 17.0.0 he02047a_3_cpu conda-forge
libarrow-substrait 17.0.0 hc9a23c6_3_cpu conda-forge
libasprintf 0.22.5 h661eb56_2 conda-forge
libasprintf-devel 0.22.5 h661eb56_2 conda-forge
libblas 3.9.0 23_linux64_openblas conda-forge
libboost 1.84.0 hba137d9_3 conda-forge
libboost-devel 1.84.0 h00ab1b0_3 conda-forge
libboost-headers 1.84.0 ha770c72_3 conda-forge
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libbrotlicommon 1.1.0 hd590300_1 conda-forge
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libcap 2.69 h0f662aa_0 conda-forge
libcblas 3.9.0 23_linux64_openblas conda-forge
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libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
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libcurl 8.9.1 hdb1bdb2_0 conda-forge
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libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.6.2 h59595ed_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libflac 1.4.3 h59595ed_0 conda-forge
libgcc-ng 14.1.0 h77fa898_0 conda-forge
libgcrypt 1.11.0 h4ab18f5_1 conda-forge
libgd 2.3.3 h119a65a_9 conda-forge
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libgfortran-ng 14.1.0 h69a702a_0 conda-forge
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libgoogle-cloud 2.26.0 h26d7fe4_0 conda-forge
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libgrpc 1.62.2 h15f2491_0 conda-forge
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mda-xdrlib 0.2.0 pyhd8ed1ab_0 conda-forge
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nomkl 1.0 h5ca1d4c_0 conda-forge
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pycparser 2.22 pyhd8ed1ab_0 conda-forge
pydantic 2.8.2 pyhd8ed1ab_0 conda-forge
pydantic-core 2.20.1 py312hf008fa9_0 conda-forge
pydot 3.0.1 py312h7900ff3_0 conda-forge
pyedr 0.8.0 pyhd8ed1ab_0 conda-forge
pygments 2.18.0 pyhd8ed1ab_0 conda-forge
pygtail 0.14.0 pyhd8ed1ab_0 conda-forge
pymbar 4.0.3 h7900ff3_1 conda-forge
pymbar-core 4.0.3 py312hc7c0aa3_1 conda-forge
pymsmt 22.0 pypi_0 pypi
pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
pytables 3.9.2 py312hf20fedc_3 conda-forge
python 3.12.4 h194c7f8_0_cpython conda-forge
python-constraint 1.4.0 py_0 conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.20.0 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.12 4_cp312 conda-forge
pytng 0.3.3 py312h39b0089_0 conda-forge
pytraj 2.0.6 pypi_0 pypi
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.1 py312h98912ed_1 conda-forge
pyzmq 26.0.3 py312h8fd38d8_0 conda-forge
qhull 2020.2 h434a139_5 conda-forge
qt-main 5.15.8 h320f8da_24 conda-forge
rdkit 2024.03.3 py312h93d94ad_0 conda-forge
re2 2023.09.01 h7f4b329_2 conda-forge
readline 8.2 h8228510_1 conda-forge
referencing 0.35.1 pyhd8ed1ab_0 conda-forge
reportlab 4.2.2 py312h9a8786e_0 conda-forge
requests 2.32.3 pyhd8ed1ab_0 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rich 13.7.1 pyhd8ed1ab_0 conda-forge
rlpycairo 0.2.0 pyhd8ed1ab_0 conda-forge
rpds-py 0.19.1 py312hf008fa9_0 conda-forge
s2n 1.4.17 he19d79f_0 conda-forge
sander 22.0 pypi_0 pypi
scikit-learn 1.5.1 py312h775a589_0 conda-forge
scipy 1.14.0 py312hc2bc53b_1 conda-forge
seaborn 0.13.2 hd8ed1ab_2 conda-forge
seaborn-base 0.13.2 pyhd8ed1ab_2 conda-forge
send2trash 1.8.3 pyh0d859eb_0 conda-forge
setuptools 71.0.4 pyhd8ed1ab_0 conda-forge
sire 2024.2.0 py312h0666ab4_0 openbiosim
six 1.16.0 pyh6c4a22f_0 conda-forge
smirnoff99frosst 1.1.0 pyh44b312d_0 conda-forge
snappy 1.2.1 ha2e4443_0 conda-forge
sniffio 1.3.1 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
sqlalchemy 2.0.31 py312h9a8786e_0 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
statsmodels 0.14.2 py312h085067d_0 conda-forge
tbb 2021.12.0 h434a139_3 conda-forge
tenacity 8.2.3 py312h06a4308_0
terminado 0.18.1 pyh0d859eb_0 conda-forge
threadpoolctl 3.5.0 pyhc1e730c_0 conda-forge
tidynamics 1.1.2 pyhd8ed1ab_0 conda-forge
tinycss2 1.3.0 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tornado 6.4.1 py312h9a8786e_0 conda-forge
tqdm 4.66.4 pyhd8ed1ab_0 conda-forge
traitlets 5.14.3 pyhd8ed1ab_0 conda-forge
types-python-dateutil 2.9.0.20240316 pyhd8ed1ab_0 conda-forge
typing-extensions 4.12.2 hd8ed1ab_0 conda-forge
typing_extensions 4.12.2 pyha770c72_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
urllib3 2.2.2 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
webcolors 24.6.0 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_2 conda-forge
websocket-client 1.8.0 pyhd8ed1ab_0 conda-forge
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
widgetsnbextension 4.0.11 pyhd8ed1ab_0 conda-forge
xcb-util 0.4.1 hb711507_2 conda-forge
xcb-util-image 0.4.0 hb711507_2 conda-forge
xcb-util-keysyms 0.4.1 hb711507_0 conda-forge
xcb-util-renderutil 0.3.10 hb711507_0 conda-forge
xcb-util-wm 0.4.2 hb711507_0 conda-forge
xkeyboard-config 2.42 h4ab18f5_0 conda-forge
xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.9 hb711507_1 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 0.9.11 hd590300_0 conda-forge
xorg-libxt 1.3.0 hd590300_1 conda-forge
xorg-libxxf86vm 1.1.5 h4bc722e_1 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zeromq 4.3.5 h75354e8_4 conda-forge
zipp 3.19.2 pyhd8ed1ab_0 conda-forge
zlib 1.3.1 h4ab18f5_1 conda-forge
zlib-ng 2.2.1 he02047a_0 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
And here is my gromacs version:
GROMACS version: 2024.2
Precision: mixed
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128)
GPU support: disabled
SIMD instructions: AVX2_256
CPU FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128
GPU FFT library: none
Multi-GPU FFT: none
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
C compiler: /usr/bin/cc GNU 11.4.0
C compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -O3 -DNDEBUG
C++ compiler: /usr/bin/c++ GNU 11.4.0
C++ compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -O3 -DNDEBUG
BLAS library: Internal
LAPACK library: Internal
Thanks a lot!
Thanks!
Turns out the issue is caused by using the latest version of GROMACS. When I upgrade to 24.2, I can reproduce this error. Printing the error inside the try/except block which raises the BSS warning shows:
ValueError: Failed to construct topology from file .../05_npt_relax/restraint_search/gromacs.tpr with parser <class 'MDAnalysis.topology.TPRParser.TPRParser'>.
Error: Your tpx version is 133, which this parser does not support, yet
Because MDAnalysis 2.7.0 is does not support the newest GROMACS tpx format (see the relevant PR here). To get round this you need to install the latest development version of MDAnalysis, which is not available on conda forge. To do this, first remove your current version of MDAnalysis with
conda remove --force mdanalysis
This removes only MDAnalysis, but I think the behaviour is different if you use mamba (you can install conda in your mamba environment if so). Then clone the MDAnalysis github repo and install from source:
git clone https://github.com/MDAnalysis/mdanalysis.git
cd mdanalysis/package
pip install .
Then your script should work fine with GROMACS 24.2.
No problem!