Dear all,
I have AmberTools 23 installed through the source on a cluster, and recently one of my users reported the following when using packmol-memgen:
Traceback (most recent call last):
File "/progs/all/opensource/ambertools/23/bin/packmol-memgen", line 189, in <module>
packmol_memgen.main(args)
File "/progs/all/opensource/ambertools/23/lib/python3.10/site-packages/packmol_memgen/main.py", line 895, in main
grid = pdbvol(pdb)
File "/progs/all/opensource/ambertools/23/lib/python3.10/site-packages/packmol_memgen/main.py", line 784, in pdbvol
atoms = pdbatoms.read_pdb("temp.pdb")
File "/progs/all/opensource/ambertools/23/lib/python3.10/site-packages/packmol_memgen/lib/pdbremix/pdbatoms.py", line 212, in read_pdb
atoms.append(AtomFromPdbLine(line))
File "/progs/all/opensource/ambertools/23/lib/python3.10/site-packages/packmol_memgen/lib/pdbremix/pdbatoms.py", line 128, in AtomFromPdbLine
atom = Atom()
File "/progs/all/opensource/ambertools/23/lib/python3.10/site-packages/packmol_memgen/lib/pdbremix/pdbatoms.py", line 43, in __init__
self.pos = v3.vector() if pos is None else pos
File "/progs/all/opensource/ambertools/23/lib/python3.10/site-packages/packmol_memgen/lib/pdbremix/v3numpy.py", line 29, in vector
return np.zeros(3, dtype=np.float)
File "/progs/all/opensource/ambertools/23/miniconda/lib/python3.10/site-packages/numpy/__init__.py", line 305, in __getattr__
raise AttributeError(__former_attrs__[attr])
AttributeError: module 'numpy' has no attribute 'float'.
`np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations. Did you mean: 'cfloat'?
I did not change any parameters other than the prefix, so I assume the code just needs to be updated to match the more recent version of NumPy. The one that gets installed on my system is version 1.24. Or is there something that I should change from the installation perspective?
Thank you,
João
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Received on Tue Aug 08 2023 - 02:30:02 PDT
