VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Oct 16 2013 - 14:34:23 CDT

Hi,

did you try loading the PSF file first, then the PDB?

Jerome

----- Original Message -----
> 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
>