Debugging

Troubleshooting common PyMACS problems

Most first failures are caused by environment, folder, input-file, ligand-name, or topology mismatches. Check the simple things before changing scientific settings.

First commands to run

Copy command 
pwd
ls
python --version
gmx --version
find . -maxdepth 2 -type f | sort | head -80

Common problems

Symptom Likely cause
python: command not found Python is not available in the active shell.
conda: command not found Conda is not installed or not initialized.
gmx: command not found GROMACS is not installed, loaded, or visible on PATH.
Script cannot find the input file You are in the wrong folder or did not copy the input file.
Ligand parameters missing The .str or .cgenff.mol2 file is absent or named differently from the ligand code.
grompp fails Topology mismatch, atom-name mismatch, missing parameter, or incompatible MDP/index selection.
No plots appear Analysis did not finish or Analysis_Results was written somewhere else.

What to save when asking for help

  • The exact command you ran.
  • The last 20-30 terminal lines before the error.
  • The current folder from pwd.
  • A file listing from ls.
  • Relevant log files such as mdrun.log or grompp output.