VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Sep 30 2003 - 12:48:26 CDT

Hi,

The following VMD commands should clean up your pdb file:

set mol [mol load pdb Au.pdb]
set all [atomselect $mol all]
$all set resname Au
$all set segid Au
set resid {}
set i 0
foreach a [$all get index] {
  lappend resid [incr i]
}
$all set resid $resid
$all writepdb new.pdb

This is what new.pdb looks like at the end:

CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ATOM 1 Au Au X 1 0.000 0.000 0.000 0.00 0.00 Au
ATOM 2 Au Au X 2 0.862 -1.491 -2.313 0.00 0.00 Au
ATOM 3 Au Au X 3 1.848 -2.193 0.305 0.00 0.00 Au
...

-Jim

On Tue, 30 Sep 2003, FOK LO MING wrote:

> Hi,
>
> I would like to convert a pdb file into psf format using the
> psfgen, as there is no residue in the pdb file, it is unable to segment
> the pdb file so that no psf file could be generated. Could someone help me
> in solving this problem? Thank you very much.
>