Hi,
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,
-Dan
On Mon, Oct 4, 2021 at 11:33 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 Thu Oct 14 2021 - 07:30:03 PDT
