After running this step to create ligand topology for molecular dynamic simulation protein-ligand complex:
python3 cgenff_charmm2gmx_py3_nx2.py ligand ligand_fix.mol2 ligand.str charmm36-jul2022.ff
It showed some tracebacks and import error:
ImportError: cannot import name 'gcd' from 'fractions' (/usr/lib/python3.10/fractions.py)
Does anybody know how to fix this problem in Ubuntu with python3.10 version?
#gromacs #topology #moleculardynamics
try webservers i.e., Ligpargen or swissparam, hope it will work for you
Install latest version of networkx (> 2.5) and try to run again.
I have python 3.5.2, networkx 2.3 and numpy-1.25.0 all installed, the error persists, now i get the message
File "cgenff_charmm2gmx_py3_nx2.py", line 53, in
import numpy as np
ImportError: No module named 'numpy'
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