Re: [AMBER] How to superpose the solvated box to the original pdb structure?

From: Song, Lin <songlin3.chemistry.msu.edu>
Date: Tue, 5 Oct 2021 04:33:34 +0000

Hi Zhenting,

You can take a look at the cpptraj tutorials.

Best,
Lin

> On Oct 4, 2021, at 11:32 PM, Gao Zhenting <zhentgpicasa.gmail.com> wrote:
>
> Dear Amber users,
>
> After solvating the protein into a box, the original coordinates of the
> protein are changed. Is there any way to superpose the solvated system to
> the original pdb structure, so that it is easier to compare the trajectory
> with the original pdb conformation?
>
> Regards
> Zhenting
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Received on Mon Oct 04 2021 - 22:00:03 PDT