From: Isuru Herath (
Date: Wed Jan 20 2021 - 21:12:31 CST


I am having trouble coarse graining a protein that contains CA+2 and MG+2
ions in its structure with MARTINI. I tried using CHARMM-GUI's Martini
Maker but that ignores non-protein atoms. Also the CG Builder on VMD does
not assign specific secondary structures. Any help would be appreciated.

Thank you,
Isuru Herath