VMD-L Mailing List
From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Thu Jan 21 2021 - 00:48:57 CST
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The lipopolysaccharide CG model in CHARMM-GUI uses a CG of Ca ions. That could be a good way to start with.
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________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Isuru Herath <ish9_at_cornell.edu>
Sent: Thursday, January 21, 2021 8:42:31 AM
To: VMD Mailing LIst <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Coarse-Graining Protein with Ion Ligands
Hello,
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
- Next message: Maria Dimitrova: "OpenGL window not rendering over ssh but works when connecting from other computers and works fine locally"
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- In reply to: Isuru Herath: "Coarse-Graining Protein with Ion Ligands"
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