From: Jim Parker (jimparker96313_at_gmail.com)
Date: Wed Oct 16 2013 - 13:20:30 CDT

Hello,
  I am trying to select a subset of atoms from a trajectory to carry
forward in another set of simulations.

My unsuccessful method:
I had loaded the associated .pdb, .psf, and .dcd files into VMD and used
the atomselect function to choose an appropriate subset.I then used the
commands

$sel writepdb "foo.pdb
$sel writepsf "foo.psf"

To make the new starting structures. The .pdb file is fine. However, the
.psf file does not name the atoms correctly.

For example, the original .psf file had:
      2 A 1 LEU HT1 HC 0.330000 1.0080 0
but in foo.psf, the new line is
      2 A 1 LEU HT1 HT1 0.330000 1.0080 0

Basically, the writepsf algorithm just echoes the atom name into the atom
type column, which generates a useless .psf file as the names are not found
in the parameters.

I had expected that the writepsf function would take the correct values
from the original .psf that was loaded into VMD.

 Note: I'm not using the psfgen comand writepsf, but the function
associated with atomselect per the VMD manual
http://www.ks.uiuc.edu/Research/vmd/current/ug/node121.html

Can someone tell me what I'm doing wrong to use this command?

I could use psfgen, but this method would be much easier, as I wouldn't
have to break down the molecule into segments and re-patch.

System parameters
vmd-1.9.1
Linux 64-bit Ubuntu 12.04

Cheers,
--Jim Parker