AMBER Archive (2009)

Subject: [AMBER] setBox truncated octahedron

From: Myunggi Yi (
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?

Best wishes,

Myunggi Yi ================================== KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306

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