environment.yaml pulls new versions of packages that probably don't work together with this code #24
Description
Is it possible to provide a list of package versions that once worked and can now be pinned? I find that the scripts here are not working and I am guessing the issues are related to changes to package versions newer than this one.
- Creating the env and attempting to run prep_SepTop_solvent.py gives me the error:
File "/Users/chrisneale/opt/anaconda3/envs/septop/lib/python3.12/site-packages/openff/toolkit/utils/ambertools_wrapper.py", line 64, in __init__ ambertools_version = out.decode("utf-8").split("\n")[1].split()[3].strip(":")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^
IndexError: list index out of range
When I run 'antechamber -L' I get output that doesn't have the version info but instead a blank line on line 2. Presumably I am getting AmberTools 24.8 now and before maybe the second line was not empty?
$ antechamber -L
List of the File Formats
file format type abbre. index | file format type abbre. index
--------------------------------------------------------------
Antechamber ac 1 | Sybyl Mol2 mol2 2
I can fix this simply by modifying site-packages/openff/toolkit/utils/ambertools_wrapper.py near line 64 to set ambertools_version = 'unknown' instead of trying to parse it.
- After fixing that, I get the error below. I'm not sure yet if that is a package issue or if I did something wrong, but having a list of pinned package versions that should work would really help here so that I could know that it should work.
File "/Users/chrisneale/opt/anaconda3/envs/septop/lib/python3.12/site-packages/parmed/gromacs/gromacstop.py", line 1060, in parametrize
atom.atom_type = params.atom_types[atom.type]
~~~~~~~~~~~~~~~~~^^^^^^^^^^^
KeyError: 'dLIG2_O2D'
Thank you,
Chris.