Ligand preparation code error

User discussions
1

GROMACS version: 2021.4-Ubuntu-2021.4-2
GROMACS modification: Yes/No
Here post your question
when i enter this code to create ligand topology files it shows an error. I have networkx version 2.3, python 3.10.6. can anyone help me to fix this issue?

entered code:

python3 cgenff_charmm2gmx_cp.py JZ4 jz4_fix.mol2 jz4.str charmm36-jul2021.ff"

Error found:

Traceback (most recent call last):
File “/media/omar/Secondary/MDs/test/cgenff_charmm2gmx_cp.py”, line 54, in
import networkx as nx
File “/usr/local/lib/python3.10/dist-packages/networkx/init.py”, line 114, in
import networkx.generators
File “/usr/local/lib/python3.10/dist-packages/networkx/generators/init.py”, line 14, in
from networkx.generators.intersection import *
File “/usr/local/lib/python3.10/dist-packages/networkx/generators/intersection.py”, line 13, in
from networkx.algorithms import bipartite
File “/usr/local/lib/python3.10/dist-packages/networkx/algorithms/init.py”, line 16, in
from networkx.algorithms.dag import *
File “/usr/local/lib/python3.10/dist-packages/networkx/algorithms/dag.py”, line 23, in
from fractions import gcd
ImportError: cannot import name ‘gcd’ from ‘fractions’ (/usr/lib/python3.10/fractions.py)

2

Some syntax has changed between Python versions. Use an older Python version (e.g. 3.7.x).

3

Thank you so much for your time, but i have python 3.10.6 default in my ubuntu 22.04 LTS, can you explain how can i use 3.7 instead of 3.10.6? or run the script in 3.10.6? This will be so helpful for me,

4

Are you familiar with installing packages using conda? Or using conda to setup an environment with specific versions of a package? (Managing environments — conda 23.7.2.dev9 documentation)

5

not that much, but i have conda installed in my system, i’ll try to do this and get an updt