AMBER Archive (2009)
Subject: [AMBER] setBox truncated octahedron
From: Myunggi Yi (myunggi_at_gmail.com)
Date: Thu Jun 11 2009 - 12:27:26 CDT
Dear Amber users,
I have coordinates of a pre-equilibrated protein in a truncated octahedral
After a minor modification of the PDB file, I prepared the TOP and CRD files
with setBox options using leap.
Then I modified the box information in the TOP file and the bottom of the
CRD file to get truncated octahedral box.
Now I am getting a strange water box which is not even a rectangular or
truncated octahedral box.
Is there a way to solve this problem?
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306
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