Re: [AMBER] Superimpose

From: mohamed marzouk <>
Date: Sat, 27 Mar 2021 10:57:47 +0000

Thank too much.
Very clear now, much helpful.

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From: Daniel Roe <>
Sent: Friday, March 5, 2021 4:06:11 AM
To: AMBER Mailing List <>
Subject: Re: [AMBER] Superimpose


I think you're conflating imaging with superposition (best-fit
alignment). Imaging is moving things back into the primary unit cell.
Superposition is aligning the system to a reference. Commands like
'image' and 'autoimage' relate to the former; commands like 'rms' and
'align' relate to the latter.

You can do both, but unless you're running cpptraj version 5 or above
you need to do imaging before rms-fitting. So say I have a DNA
dodecamer in solvent and I want to image and best-fit to the structure
in the first frame and remove the solvent. I would do something like
this in cpptraj:

parm myparm.parm7
strip :WAT parmout strip.parm7
autoimage origin
box nobox
align first :1-24&!.H=

The resulting trajectory '' can be used with the
corresponding topology 'strip.parm7'. Hope this helps,


On Mon, Mar 1, 2021 at 1:11 PM mohamed marzouk
<> wrote:
> Hello AMBER users,
> I want to do superimpose for dissociation trajectory with respect to DNA, How?!
> I check the autoimage parameters, but I have question. My system (DNA, protein, and ions) I want to superimpose the trajectories where DNA keep the same position every frame of the traj. and protein moving without any alignemnt as my target is dissociation of protein and sure Ions and water. The Q?! Anchor : DNA , mobile region: ions , fixed is protein ?! Are these right parameters for auto images ?!
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Received on Sat Mar 27 2021 - 04:00:01 PDT
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