From: Raman Preet Singh (
Date: Thu Jan 21 2021 - 00:48:57 CST

The lipopolysaccharide CG model in CHARMM-GUI uses a CG of Ca ions. That could be a good way to start with.

Get Outlook for Android<;!!DZ3fjg!tLJNPseMT-GTYmDs9tIeaodKWVcHsQrt9URrNIvk-4wv7sOBKBeAsEXlg7naVfpl5g$ >

From: <> on behalf of Isuru Herath <>
Sent: Thursday, January 21, 2021 8:42:31 AM
To: VMD Mailing LIst <>
Subject: vmd-l: Coarse-Graining Protein with Ion Ligands


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