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

From: Dr. Anselm Horn <>
Date: Tue, 5 Oct 2021 10:51:03 +0200

Hi Zhenting,

if solvation changed your coordinates, this should only affect
transitions and rotations of your system, but no internal coordinates.
Thus, when you simply use the solvated structure as reference for
cpptraj analyses of your trajectory results, it should be fine.

If you want to check for yourself, that your original pdb structure and
the solvated pdb structure are essentially the same, you could also use
superimposition and RMSD calculation features in common molecular
viewers like VMD or chimera.



PD Dr.rer.nat.
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg

Am 05.10.2021 um 06:33 schrieb Song, Lin:
> Hi Zhenting,
> You can take a look at the cpptraj tutorials.
> Best,
> Lin
>> On Oct 4, 2021, at 11:32 PM, Gao Zhenting <> 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 Tue Oct 05 2021 - 02:00:02 PDT
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