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

From: David A Case <>
Date: Tue, 5 Oct 2021 08:40:42 -0400

On Tue, Oct 05, 2021, Gao Zhenting wrote:

>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?

You can use "set default nocenter on" to keep tleap from moving the
coordinates upon setup. But, of course, the system will "drift" as you run
MD, so something like cpptraj is needed to superpose the system back to the
original coordinates.


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Received on Tue Oct 05 2021 - 06:00:03 PDT
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