VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Oct 16 2013 - 14:37:33 CDT

Hi Jim,

This is actually a subtle problem present in 1.9.1 (and may have been
fixed now, I'm not sure). What you did was load the pdb file before the
psf file. When that happens, VMD loads the atomtype from the atomnames
column of the pdb instead of the psf that is loaded afterwards, since I
think the filereader is trying to be careful and not clobber data that
already exists. The fix is to be careful when loading your molecule to
load psfs before pdbs. The atomselection writepsf command should still
be used with caution in 1.9.1, as it will not write out extended format
PSFs when required.

-Josh Vermaas

On 10/16/2013 01:20 PM, Jim Parker wrote:
> 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
>