VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Dec 17 2007 - 11:50:12 CST

Hi,

The psfgen coordpdb command is intended to read coordinates into a
structure. It doesn't actually load or build the structure. If you try
to set coordinates for an atom that doesn't exist, it gives you a warning
and ignores the command. It doesn't actually create the atom in psfgen.

Since all you want to do is delete some atoms from a pdb file, you don't
need psfgen at all. VMD atom selections have a writepdb command (actually
they have a writeXXX command, where XXX is any known format). Your
solution is:

set sel [atomselect top "atoms you want to keep"]
$sel writepdb keep.pdb
$sel delete

-Jim

On Sun, 9 Dec 2007, Stephen M. Dutz wrote:

> I then wrote the following code which calls the combined protein and
> lipid file popc_cff.pdb
>
>
>
> package require psfgen
>
>
>
> #load combined file into vmd and psfgen
>
> resetpsf
>
> coordpdb popc_cff.pdb
>
> However it continually outputs the following error:
>
>
> Warning: failed to set coordinate for atom C40 POP:97 L
>
> no segment L
>
>
>
> It seems that although the script pulls the segid "L", when it goes to
> use this with the delatom command it does not recognize a segment L. Is
> this problem occurring because I am not using any psf files? Any help
> would be much appreciated.
>
>
>
> Thanks in advance,
>
>
>
> Steve
>
>