Re: fix backbone atom

From: JC Gumbart (
Date: Sun Oct 09 2005 - 02:29:57 CDT

The appendix of the NAMD tutorial outlines the structure of pdb files
in general. There are two columns typically used (at least for NAMD)
to modify properties of individual atoms, the occupancy and beta
columns. If you look at your pdb closely, you will notice that all
numbers in the 2nd to last column (or at least the 2nd column after the
coordinates, the beta column) are 0 except for the ones for the protein
backbone which are 1.

Then in the configuration file for NAMD, you would specify that some
atoms are to be fixed and to look in file test1-fix_backbone.pdb at the
beta column to know which ones.

On Oct 9, 2005, at 1:52 AM, bo baker wrote:

> 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
> Bo

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