AMBER: Trajectory problems

From: Steve Seibold <>
Date: Thu, 17 Mar 2005 16:44:23 -0500

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 - 21:53:00 PST
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