mecky@DESKTOP-P2C3VM2:/mnt/c/cta-ns2$ python3 cgenff_charmm2gmx.py UNK unk_fix.mol2 unk.str charmm36-jul2022.ff
Traceback (most recent call last):
File "/mnt/c/epigall-ns2/cgenff_charmm2gmx.py", line 54, in
import networkx as nx
File "/home/mecky/.local/lib/python3.10/site-packages/networkx/__init__.py", line 84, in
import networkx.generators
File "/home/mecky/.local/lib/python3.10/site-packages/networkx/generators/__init__.py", line 5, in
from networkx.generators.classic import *
File "/home/mecky/.local/lib/python3.10/site-packages/networkx/generators/classic.py", line 21, in
from networkx.algorithms.bipartite.generators import complete_bipartite_graph
File "/home/mecky/.local/lib/python3.10/site-packages/networkx/algorithms/__init__.py", line 12, in
from networkx.algorithms.dag import *
File "/home/mecky/.local/lib/python3.10/site-packages/networkx/algorithms/dag.py", line 2, in
from fractions import gcd
ImportError: cannot import name 'gcd' from 'fractions' (/usr/lib/python3.10/fractions.py)
mecky@DESKTOP-P2C3VM2:/mnt/c/cta-ns2$
Maybe this could help - https://stackoverflow.com/questions/66174862/import-error-cant-import-name-gcd-from-fractions
This error may be related to the python version.
Replace "from fractions import gcd " with "from math import gcd".I guess it's useful.
@Huiling Zhang, thanks for your response. I resolved the issue by simply tapping the space bar to align the ligand.gro file when pasting it in protein.gro file. Any misalignment of the table leads to fatal error.
Gromacs is so error prone to say the least. It's like there's an issue waiting every step of the way. Now I have a new trouble, my ionization of the complex does not work. It returns the error message below:
ERROR 1 [file topol.top, line 71115]:
No such moleculetype UNK_preprocessed
There was 1 note
Program: gmx grompp, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 2512)
Fatal error:
There was 1 error in input file(s)
Any help is appreciated. Thanks
The error occurs because fractions.gcd was removed in Python 3.9+. Replace fractions.gcd with math.gcd in dag.py, or downgrade to Python 3.8.
All of which can we easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.
- Badges
- Science topic
- Similar topics
- Biological Science
- Microbiology