VMD-L Mailing List

From: Jim Parker (jimparker96313_at_gmail.com)
Date: Wed Oct 16 2013 - 18:25:32 CDT

Josh and Jerome,
  Your guess was correct! I was loading the .pdb first. Changed the
order, and it all looks good. Josh, I will heed your warning with regards
to writepsf, but in this case it seems to work.

Thank you both.

Cheers,
--Jim

On Wed, Oct 16, 2013 at 2:37 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> 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
>
>
>
>