AMBER Archive (2009)

Subject: Re: [AMBER] problems with ptraj option IMAGE

From: Carlos Simmerling (
Date: Mon Jun 29 2009 - 10:00:59 CDT

do the center command first, then image.

> 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.
> Gratefully
> Antonija
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