AMBER Archive (2009)

Subject: [AMBER] problems with ptraj option IMAGE

From: Antonija Tomić (
Date: Mon Jun 29 2009 - 09:48:54 CDT


I have some problems with ptraj option IMAGE and I would be very
grateful if someone could help me.
I have an enzyme and I am trying to put waters back in truncated
octahedron (I have made truncated octahedron using Leap and distance
parameter of 7 angstroms). When I use:

trajin mol-name.rst
image origin center familiar
center :1-11431 mass origin
trajout mol-nameOUT.crd

I get water box with a shape of truncated octahedron but my enzyme is
half in and half out of that box. I do not know if I can use prtaj to
put back waters in truncated octahedron such that the closest distance
between any atom of the solute and the edge of the solute box is 7
angstroms (like Leap). I do not know if this is possible or you can
suggest me to do something else.


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