I created the .str file for my ligand (7LD) by uploading the .mol2 file on CGenff. When executing:
python cgenff_charmm2gmx.py 7LD 7LD_fix.mol2 7LD.str charmm36-feb2021.ff
I get the error:
IndexError: list index out of range?
Can this be because my parampenalty is 68? Any help is appreciated.
Dear Zahra Alavi
It seems an error associated with python itself rather than the parametrization quality.
Check your networkx version (http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs) and downgrade if it is not correct. I had the same issue and solved it by installing the correct one.
Hope this helps,
Nicola
Dear Alvi,
Your network version and Python should correlate; else, you can edit your script before passing.
The suggestion is to check the network version and reinstall it.
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Programming Languages
- Python