RE: How do you specify which coordinates are to be fixed?

From: Blake Charlebois (
Date: Thu Oct 28 2004 - 17:36:56 CDT

Hi Charles,

Did you specify "fixedAtomsCol B" in your configuration file? The default is
occupancy (O).

To get a list of every beta or occupancy value in your PDB file,
1) load it in VMD,
2) open the graphics window,
3) choose the selections tab,
4) choose beta or occupancy in the keywords box.

A list of values will appear in the value box.


-----Original Message-----
From: [] On Behalf
Of Charles Danko
Sent: October 28, 2004 5:44 PM
Subject: namd-l: How do you specify which coordinates are to be fixed?


Question: I am trying to do a dynamics run with a fixed protein but
allowing the water and lipid to equilibrate around the structure. How
do I build the pdb file which fixes all atoms except the protein?

I have tried a suggestion found on a webpage in a slightly different
context, but the result is that all atoms in the system are fixed.
The details of what I have already tried is listed below:

To fix the system, I am using very simple commands:
fixedAtoms on
fixedAtomsFile CONS.pdb

I used VMD to build CONS.pdb, with the following commands at the
suggestion of a webpage I found.
> mol load psf SYSTEM.psf pdb SYSTEM.pdb
> atomselect top all
> atomselect0 set beta 0
> atomselect top {protein}
> atomselect1 set beta 1
> atomselect0 writepdb CONS.pdb

If I load the pdb file, I can set color-mode to beta, and the protein
is blue while the rest of the system is red.

Under the structure summary, I am receiving the message
Info: 66547 atoms
Info: 66547 fixed atoms

Thanks for the help,

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