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

From: Reyes Nuñez Franco <>
Date: Tue, 5 Oct 2021 11:21:06 +0000

Hi Zhenting,

I didn't fully understand what you tried to do by aligning the original PDB to the solvated protein, but maybe what you could do is to save a pdb after the GIST calculation, so you have it oriented in the same way as the one used for the calculation.
You can try using 'trajout ref-frame.pdb onlyframes 1', in that way you will extract the first frame of your trajectory oriented in the same way as for the GIST calculation.

I hope this helps you!


Reyes Núñez Franco (PhD student)

-----Mensaje original-----
De: Gao Zhenting <>
Enviado el: 05 October 2021 13:04
Para: AMBER Mailing List <>
Asunto: Re: [AMBER] How to superpose the solvated box to the original pdb structure?

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Hi Lin and Anselm,

Thanks for your help.
I get your point regarding the cpptraj operations.

My goal is to get a solvated box with protein coordinates aligned to the original pdb file, before MD simulation.
Why I want to do this?
I am learning GIST, and of the tutorial(, solute heavy atoms(protein) are restrained, so there is no translational and rotational movement during the simulation.
 When it is to define the region for GIST analysis, the ligand is co-crystal pdb is used as reference.
 Since the solvated box does not align to the original pdb, I have to generated the pdb file of the solvated system(use "ambpdb"), align the original PDB to the solvated protein, and then save the coordinates of the aligned ligand. This is not a big deal, but if I can have the solvated protein aligned to the original pdb at the beginning, then I don't need to do all these stuffs.

Any further thoughts?


Dr. Anselm Horn <> 于2021年10月5日周二 下午4:52写道:

> 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.
> Regards,
> Anselm
> PD Dr.rer.nat.
> Bioinformatik | NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg Germany
> 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
> >> _______________________________________________
> >> AMBER mailing list
> >>
> >>
> >
> >
> > _______________________________________________
> > AMBER mailing list
> >
> >
> >
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Received on Tue Oct 05 2021 - 04:30:03 PDT
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