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

From: Luis Rosales (
Date: Thu Oct 28 2004 - 18:32:28 CDT

Hi Charles:

I think that your commands:

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

Should work if you change them for:

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

A similar code worked for me, on a simulation with my protein fixed and the
solvent unfixed.
Anyway, if you havent, maybe a visit to the NAMD hands on tutorial
(, will
help you.

Good luck!


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:57 CST