Re: AMBER: Trajectory problems

From: Asim Okur <>
Date: Thu, 17 Mar 2005 18:14:28 -0500


if i remember your script from previous e-mail correctly you should use
nobox command on your output trajectory when stripping water. If not
ptraj will keep the box information on the trajectory.

Then when you calculate RMSD you need to use a topology file without the
solvent which is consistent with the stripped trajectory.

I hope this helps ,


Asim Okur
Stony Brook University
Chemistry Department
Stony Brook, NY 11794-3400
631 - 632 1560
Steve Seibold wrote:
> Hello AMBER users
> Thanks, Melinda
> Indeed, I had forgotten to change my topology file to one without 
> water although I created one for that very purpose! Ugh. However, I 
> was working on another problem originally when I slipped into using 
> the incorrect topology file.
> The problem is that I cannot get RMSd values for my protein after I 
> strip it of waters EVEN when I use the correct topology file. I get 
> messages about the lack of box information in the output file. I get 
> the same complaint from AMBER if I specifically write in the box size 
> info in the input script or if I get AMBER to remove box info using 
> “nobox” in script. I thought without waters I did not need box 
> information. Even so, the trajectory files do have the box info at the 
> bottom of the file even after I strip out the waters(not using nobox 
> here). So I am confused about its complaint that it cannot find the 
> box info.
> Can someone tell me what I am doing incorrectly?
> Thanks, Steve
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Received on Thu Mar 17 2005 - 23:53:00 PST
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