/home/miniconda3/envs/AmberTools22/lib/python3.10/site-packages/parmed/gromacs/gromacstop.py:1022: GromacsWarning: 25 1-4 pairs were missing from the [ pairs ] section and were set to zero; make sure you know what you're doing!
warnings.warn('%i 1-4 pairs were missing from the [ pairs ] '
Traceback (most recent call last):
File "/home/xjw/fe2og/prepare-akg/top/akg.py", line 4, in <module>
gmx_top = pmd.load_file('akg.itp', xyz='akg.gro')
File "/home/miniconda3/envs/AmberTools22/lib/python3.10/site-packages/parmed/formats/registry.py", line 213, in load_file
return cls(filename, *args, **kwargs)
File "/home/miniconda3/envs/AmberTools22/lib/python3.10/site-packages/parmed/gromacs/gromacstop.py", line 255, in __init__
f = load_file(xyz, skip_bonds=True)
File "/home/miniconda3/envs/AmberTools22/lib/python3.10/site-packages/parmed/formats/registry.py", line 196, in load_file
return cls.parse(filename, *args, **kwargs)
File "/home/miniconda3/envs/AmberTools22/lib/python3.10/site-packages/parmed/gromacs/gromacsgro.py", line 188, in parse
leng, ang = box_vectors_to_lengths_and_angles(
File "/home/miniconda3/envs/AmberTools22/lib/python3.10/site-packages/parmed/geometry.py", line 131, in box_vectors_to_lengths_and_angles