How do you specify which coordinates are to be fixed?

From: Charles Danko (
Date: Thu Oct 28 2004 - 16:44:21 CDT


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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