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

From: Daniel Roe <>
Date: Thu, 14 Oct 2021 10:21:14 -0400


You could try aligning the structure to the PDB using C-alpha atoms,
then reimaging any solvent/ions. Something like:

# Load structure from leap
parm myparm.parm7
trajin mycoords.rst7
# Load original PDB
parm mypdb.pdb
reference mypdb.pdb parmindex 1
# Align coords to PDB using CA atoms
align reference .CA
# Reimage any water/ions. Add the familiar keyword for truncated
octahedron cell.
image :WAT byres
# Output reimaged coords
trajout mycoords.imaged.rst7

Hope this helps,


On Mon, Oct 4, 2021 at 11:33 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

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Received on Thu Oct 14 2021 - 07:30:03 PDT
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