fix backbone atom

From: bo baker (
Date: Sun Oct 09 2005 - 01:52:35 CDT

Hello, NAMD:

I followed the tutorial of 'building Gramicidin A' to create a pdb
file with protein backbone atom fixed. My system contains protein,
lipids and water, namded as 'test1.pdb'. Here is how I did in VMD:

mol load psf test1.psf pdb test1.pdb
set all [atomselect top all]
set to_fix [atomselect top "protein and backbone"]
$all set beta 0
$to_fix set beta 1
$all writepdb test1-fix_backbone.pdb
Then I read the ' test1-fix_backbone.pdb'  using 'wordpad'. The file
is almost identical to the oringinal one 'test1.pdb'. I wonder how
NAMD could figure out the protein backone atoms are fixed based on
this .pdb coordinates.
Thanks for your advice

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