the command: python3 cgenff_charmm2gmx_py3_nx2.py UNL1 UNL_fix.mol2 UNL_fix.str charmm36-jul2022.ff
error message:
Traceback (most recent call last):
File "cgenff_charmm2gmx_py3_nx2.py", line 54, in
import networkx as nx
File "/home/citraha/.local/lib/python3.8/site-packages/networkx/__init__.py", line 117, in
import networkx.readwrite
File "/home/citraha/.local/lib/python3.8/site-packages/networkx/readwrite/__init__.py", line 15, in
from networkx.readwrite.graphml import *
File "/home/citraha/.local/lib/python3.8/site-packages/networkx/readwrite/graphml.py", line 314, in
class GraphML(object):
File "/home/citraha/.local/lib/python3.8/site-packages/networkx/readwrite/graphml.py", line 346, in GraphML
(np.int, "int"), (np.int8, "int"),
File "/home/citraha/.local/lib/python3.8/site-packages/numpy/__init__.py", line 305, in __getattr__
raise AttributeError(__former_attrs__[attr])
AttributeError: module 'numpy' has no attribute 'int'.
`np.int` was a deprecated alias for the builtin `int`. To avoid this error in existing code, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
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
The error message you provided indicates that there is an issue with the numpy library used by the networkx package. The specific problem is related to the use of np.int, which was a deprecated alias for the built-in int in NumPy.
To solve this issue, you have a few options:
pip install --upgrade numpy
2. Modify the affected code: If for some reason, you cannot upgrade numpy, you can modify the affected code to use the built-in int instead of np.int. You need to locate the file "graphml.py" in the "networkx" package and change the references to np.int to int. The file path should be "/home/citraha/.local/lib/python3.8/site-packages/networkx/readwrite/graphml.py".Open "graphml.py" in a text editor and search for np.int, then replace it with int. Do this for all occurrences in the file.
3.Use a different version of networkx: It's possible that the specific version of networkx you have installed is not fully compatible with your current numpy version. You can try installing an older or newer version of networkx to see if that resolves the issue. For example:
pip install networkx==2.6.3
or
pip install networkx==2.7
Be cautious with version changes, as it may introduce other compatibility issues with your existing code or dependencies.
Remember to create a backup of the "graphml.py" file before making any modifications, and try the solutions in the order presented above. If one solution doesn't work, proceed to the next one. Also, ensure that you have the necessary permissions to modify the files in the specified directory.
thank you very much for your recommendation! i have solved this issue! my python cannot read my networkx package before, so i uninstalled the python and networkx 2.6.3 and reinstalled both in the same path, and the problem solved!
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