AMBER Archive (2008)

Subject: Re: AMBER: problem with traj and strip waters

From: Carlos Simmerling (
Date: Thu Sep 18 2008 - 08:19:17 CDT

Steve- you're running ptraj on the combined, stripped traj file? and you're
using a no water prmtop?
you still need to have nobox at the end of your trajout line when you make
the stripped traj file.
here is a sample workflow:

ptraj using solvated prmtop
read solvated traj files
image command if needed (dimer etc)
strip water
trajout newfile nobox

ptraj using no water prmtop
read no water traj file from above
calculate rmsd

if you want to check that the prmtop and stripped traj file work together,
try using the no water prmtop in vmd and load the traj files as amber
coordinates (not amber with box)

On Thu, Sep 18, 2008 at 9:08 AM, Steve Seibold <>wrote:

> Hello Amber
> I am having a similar problem which I have had in the past, but this time I
> cannot seem to over come it. I have combined trajectories and have performed
> an rms analysis without any problem. However, once I strip the waters off
> and try to perform an rms analysis, I get absurd values (70 angstroms and
> greater). I thought maybe I should use the "nobox" but there is no box
> information at the end of the trajectory files after I strip the water out;
> so, this is not causing the problem. In addition, there is no error or
> corrupt files mentioned in the output. I am also using a topology file that
> has had all waters removed (using xleap). Does anyone have any ideas about
> what is happening?
> Of course, I could just do rms evaluation with water present, but this
> takes so long. Thus, I would like to strip the water from the trajectories.
> Thanks, Steve

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