When I run the command according to the GROMACS tutorial, I got the below result
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: 3.8.5 (default, Jul 28 2020, 12:59:40)
[GCC 9.3.0]
NOTE 2: Code tested with NetworkX 2.3. Your version: 2.5
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 jz4.str : 4.4
--Version of CGenFF detected in charmm36-jul2020.ff/forcefield.doc : 4.4
NOTE 4: To avoid duplicated parameters, do NOT select the 'Include parameters that are already in CGenFF' option when uploading a molecule into CGenFF.
Traceback (most recent call last):
File "cgenff_charmm2gmx_py3_nx2.py", line 1044, in
m.read_mol2_coor_only(mol2_name)
File "cgenff_charmm2gmx_py3_nx2.py", line 904, in read_mol2_coor_only
self.G.node[atomi]['x'] = float(entry[2])
AttributeError: 'Graph' object has no attribute 'node'
Have a look at https://networkx.org/documentation/stable/install.html and https://github.com/fenderglass/Ragout/issues/51
The "G.node" accessor was deprecated in 2.4 (https://networkx.org/documentation/stable/release/release_2.4.html#deprecations), you need to change line 904 in read_mol2_coor_only to "G.nodes()". See https://networkx.org/documentation/stable/reference/classes/generated/networkx.Graph.nodes.html
If this isn't your code, you might consider letting the author know, or launching an issue on the associated Github page.
Best of luck, Tyler
Visit these links to find out
https://stackoverflow.com/questions/49348004/is-it-possible-to-delete-downgrade-python-packages-from-google-colab
https://networkx.org/documentation/stable/install.html
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