AMBER Archive (2008)

Subject: RE: AMBER: solvate without translating

From: Ross Walker (
Date: Thu Sep 25 2008 - 01:46:52 CDT

Hi Anu,


Make a note of the coordinates of the first atom in your original structure
and the coordinates it gets in the solvated structure. Take the difference
between these and that represents your offset. Then solvate the system save
the prmtop, inpcrd etc. Then you can write script to go through the inpcrd
file and add the difference you got from the original position to the origin
to all atoms. This will then give you a shifted water box with your original


I am not sure how well this will actually work in a simulation though, I
think sander might expect the corner of the box to be the origin and so you
might get some weird behavior, then again you might not, best option is to
try it and see what happens.


I am curious why you want to preserve the original coordinates of your
protein though. If it is to do comparisons to the initial structure you can
always post process your trajectory to compare back to some reference
structure using ptraj.


All the best



From: [] On Behalf Of
Anuradha Mittal
Sent: Wednesday, September 24, 2008 12:39 PM
Subject: AMBER: solvate without translating



When I solvate my protein using solvatebox in leap, the protein is
translated to 0,0,0 coordinate and waterbox is built around it. I do not
want to change the coordinates of my protein. Is there anyway of doing it?


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