Re: [AMBER] The problem for image tool in AMBER

From: Daniel Roe <>
Date: Thu, 4 May 2017 11:49:53 -0400


First, 'autoimage' is usually a better command for re-imaging your trajectory.

Second, when you have periodic boundary conditions you have to think
in terms of cell periodicity. For example, if in your first structure
(with apparently only 2 NO3- coordinating with your metal) the metal
ion is near a unit cell boundary, you could have a third NO3- nearby
that has been translated due to imaging. If after imaging you have 3
NO3- near the metal, this is probably what happened. You can also
calculate the distance of each NO3- to the metal to verify - the
'distance' command will use the minimum imaged distance.


On Wed, May 3, 2017 at 11:20 PM, 鲁俊波 <> wrote:
> Dear all:
> I have done a molecular dynamics. But I encounter a problem when I see the structure. The attached file am_cro_md.rst is my last structure of molecular dynamics trajectory, and and am_cro.prmtop are the control and top files. I convert the structure to the pdb file using cpptraj:
> trajin am_cro_md.rst
> trajout am_cro_md1.pdb
> This structure seems no periodic. So I use the image tool:
> trajin am_cro_md.rst
> image center
> trajout am_cro_md2.pdb
> This two structures are different. The metal ion coordinates with two NO3- for first structure, but with three NO3- for second structure.They are so strange. I want to choose some solvent to do QM/MM optimization. So I do not know choose which structure. Is there something wrong? Can anyone give me a help?
> With my best regards,
> Junbo
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Thu May 04 2017 - 09:00:02 PDT
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