After giving this command (python3 cgenff_charmm2gmx_py3_nx2.py ligand ligand_fix.mol2 ligand.str charmm36-jul2022.ff)- This script has been tested with NetworkX 2.3, and 2.4 is buggy.
Please install version 2.3 for best performance:
pip uninstall networkx
pip install networkx==2.3
NOTE 1: Code tested with Python 3.5.2 and 3.7.3. Your version: 3.8.10 (default, May 26 2023, 14:05:08)
[GCC 9.4.0]
NOTE 2: Code tested with NetworkX 2.3. Your version: 3.1
NOTE 3: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation:
–Version of CGenFF detected in charmm36-jul2022.ff/forcefield.doc : 4.6
WARNING: CGenFF versions are not equivalent!
ERROR: Could not detect CGenFF version. Exiting.
and when I’m trying this pip uninstall networkx
pip install networkx==2.3
I’m facing this issue
Traceback (most recent call last):
File “cgenff_charmm2gmx_py3_nx2.py”, line 54, in
import networkx as nx
File “/usr/local/lib/python3.8/dist-packages/networkx/init.py”, line 117, in
import networkx.readwrite
File “/usr/local/lib/python3.8/dist-packages/networkx/readwrite/init.py”, line 15, in
from networkx.readwrite.graphml import *
File “/usr/local/lib/python3.8/dist-packages/networkx/readwrite/graphml.py”, line 314, in
class GraphML(object):
File “/usr/local/lib/python3.8/dist-packages/networkx/readwrite/graphml.py”, line 346, in GraphML
(np.int, “int”), (np.int8, “int”),
File “/usr/local/lib/python3.8/dist-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:
NumPy 1.20.0 Release Notes — NumPy v2.0.dev0 Manual …
Kindly tell how to rectify this error!!!