From: John Stone (
Date: Mon Aug 28 2006 - 11:28:06 CDT

  When you loaded the AMBER trajectory, did you make sure to load it in
the correct mode? Some AMBER CRD trajectories have box information at
each timestep, and others do not. If you're getting strange atom indices
in your selections, you'll want to double check that you loaded the trajectory
correctly. (If it was a trajectory with box info, but you loaded it without,
then you'll see visible nonsense with bonding in the trajectory frames)
That's the main thing I'd suggest checking. Another thing you can do to
verfity correctness is to look at the system visually, make a new
obviously colored and sized VDW representation using the same
  "name O and resname WAT and within 2 of residue 0"
selection you used below, enable selection updates in the trajectory tab,
and use the trajectory timestep slider control to rock forward and back
through your trajectory to visually verify that you're actually selecting
the atoms that you think you are.

  John Stone

On Mon, Aug 28, 2006 at 12:50:33PM +0100, wrote:
> Hi
> I want to identify the water molecules within 2 angstroms of certain residues
> for each frame of a trajectory. I am using the following script:
> set sel [atomselect top "name O and resname WAT and within 2 of residue 0"]
> set n [molinfo top get numframes]
> for { set i 0 } { $i < $n } { incr i } {
> $sel frame $i
> $sel update
> $sel writepdb water_$i.pdb
> }
> However I am having problems with the numbering of the waters. For instance, for
> residue 0 and frame 0 I obtain one water molecule with the number X1546.
> However, If I apply the same script only to the pdb file corresponding to the
> frame 0, the same water molecule is now numbered 910, which is correct. It
> seems that the water molecules in the trajectory are being wrongly numbered...
> What am I doing wrong? Is there any other simple way to do this type of
> analysis? My trajectory is from amber.
> Thanks in advance
> Alexandra
> -------------------------------------------------------------
> A FCUP utiliza o sistema de webmail Horde/IMP (
> Visite:

NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email:                 Phone: 217-244-3349
  WWW:      Fax: 217-244-6078