AMBER Archive (2006)

Subject: AMBER: set a trucated octahedron box in Leap

From: Vlad Cojocaru (
Date: Mon Sep 11 2006 - 09:24:44 CDT

Dear amber users,

I have an equilibrated periodic system (truncated octahedron box) and I
want to do a very small modification of the system using Leap. In the
meantime I want to retain all info regarding periodicity (box shape and
dimensions). What I do is: make a pdb file from the top file and the
last restart file (after performing imaging in ptraj), load the new pdb
into leap, modify what I need to modify, and then save a new top and crd
file. Now, the problem is that I want to retain the box dimensions and
shape of the system into the new top and crd files. For that, if the box
was cubic, I always used setbox command in Leap to fix my box dimensions
to the desired values and to have box info in the new top file .... Now,
the problem is that setBox sets automatically a cubic box even if I give
it the angle values of 109..., it still sets them to 90.

Does anyone have any idea how to overcome this problem?


P.S. The modification is replacing one -OH group with a -H atom in my

Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298

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