Re: [AMBER] iwrap=1 issue

From: Daniel Roe <>
Date: Mon, 2 May 2016 08:40:28 -0600

On Mon, May 2, 2016 at 7:53 AM, Kenneth McGuinness
<> wrote:
> trajin 'simulationFileName.crd' 1 -1 1
> unwrap !(:WAT)
> center mass origin !(:WAT)
> autoimage origin familiar
> rams first mass !(:WAT)
> trajout 'correctedTrajFileName.crd'

Just a couple of notes on this cpptraj input:

1) The 'unwrap' and 'center' commands are unnecessary - they are
effectively wiped out by the subsequent 'autoimage' command.

2) I think you meant 'rms', not 'rams'

3) Be aware that the rotations that occur during the RMS best-fit (the
'rms' command) means you will no longer be able to perform any imaging
on that trajectory. If you need imaging, make sure you don't rms
best-fit. If you don't, you may as well get rid of the box coordinates
in the output trajectory (i.e. use the 'nobox' keyword for 'trajout').


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
(801) 585-6208 (Fax)
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Received on Mon May 02 2016 - 08:00:03 PDT
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