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Building Gramicidin A

Fix Backbone Atoms

This script creates a PDB file with beta set to 1 for all backbone atoms and 0 for all other atoms. This file will be used in NAMD to fix the backbone atoms during the first stage of minimization.

You can use the Graphics menu in VMD to color by beta and see which atoms will be fixed.

Run this step!     Continue

fix_backbone.vmd

# STEP 7: Fix Backbone

# Mark atoms to fix for initial minimization
# We'll start by fixing the protein backbone and minimizing everything else.

set all [atomselect top all]
set to_fix [atomselect top "protein and backbone"]
$all set beta 0
$to_fix set beta 1
$all writepdb fix_backbone.pdb