Re: [AMBER] Part of protein going out of the box

From: Daniel Roe <>
Date: Wed, 3 Oct 2018 13:21:38 -0400


This is a visual artifact - remember that with periodic boundary
conditions the protein is never outside the box, it's just in a
different unit cell. This issue has been discussed several times on
the Amber mailing list (try searching for 'amber protein outside box'
or something similar).

That said I recommend using the 'autoimage' command from cpptraj in
place of the 'center' and 'image' commands - it typically does a
better job of removing these visual artifacts (although it's not

On Wed, Oct 3, 2018 at 11:07 AM Leena Aggarwal <> wrote:
> Dear Amber Users
> I have equilibrated the protein-water system and after 15ns when I have
> generated the pdb file using ptraj, it appears that the part of the protein
> (intrinsically disordered protein typically looks like a random coil) comes
> out of the box.
> ptraj script used for generating the pdb file is given below:
> trajin pro_prod4.mdcrd
> center :1-42
> image center familiar
> trajout pro_prod4 pdb
> For visualization, I have attached the snapshot of the protein-water system.
> >From Leena Aggarwal
> Department of Chemistry
> University of Delhi
> Delhi
> India
> _______________________________________________
> AMBER mailing list

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Received on Wed Oct 03 2018 - 10:30:03 PDT
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