notes.md

Notes

• Notes
  • System preparation
    • PDB preparation
    • Small molecules parameterization
    • Glycosilation
  • Visualization using PyMOL

System preparation

PDB preparation

Small molecules parameterization

Glycosilation

Visualization using PyMOL

load system.prmtop; load_traj system.inpcrd, format=rst7
load system.prmtop; load_traj system.rst7, format=rst7
load system.prmtop; load_traj system.rst7, format=nc

ambpdb -p system.prmtop -c system.inpcrd -ext -conect > system.pdb

# Or use the coordinates from the last equilibration step
ambpdb -p system.prmtop -c md_equil_07.rst7 -ext -conect > system_eq.pdb

Amber topology files (parmtop) can also be used, but this might require a few tweaks:

• assign secondary structure elements with: dss polymer.protein
• remove bond between WAT H1-H2: unbond r. WAT & n. H1, r. WAT & n. H2
• when loading coordinates using restart files (rst7/netCDF), use: load_traj coords.rst7, format=nc