Re: [AMBER] autoimage and TI

From: Daniel Roe <>
Date: Tue, 24 May 2016 09:06:02 -0600

On Tue, May 24, 2016 at 8:44 AM, Khabiri, Morteza <> wrote:
> I have a system including DNA and water+ions in it with the octahedron box shape. For some reason iwrap is off and the waters and ions overflowing. In the next step, I am going to try FEP calculation on it. Before starting FEP, I am going to try warping the system by cpptraj (autoimage option) first and going to run FEP on it. So I want to be sure, would wrapping effects the coordinate or i.e thermodynamics properties of the system?

As long as periodic boundary conditions are active, coordinate
wrapping has no effect on the system. However, if you are using ASCII
trajectories and your coordinates have overflowed (i.e. you have
asterisks, '****', in your coordinate fields) there is really no
recovering from that. To avoid coordinate overflow I recommend using
NetCDF trajectories and restarts (ioutfm=1 and ntxo=2 respectively - I
believe these are the defaults as of Amber 16).

One more thing to keep in mind: do *not* perform any kind of
RMS-fitting before imaging. Otherwise your coordinates will be rotated
out of alignment with your unit cell axes and imaging will not be

Hope this helps,


> Thanks
> Morteza
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
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Received on Tue May 24 2016 - 08:30:02 PDT
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