AMBER Archive (2006)

Subject: AMBER: aligning polymer with Z-axis of periodic box

From: Kenley Barrett (
Date: Wed Mar 08 2006 - 15:59:18 CST

Dear AMBER community,

I am simulating a helical polymer using explicit solvent and periodic
boundary conditions. Due to some stuff that I want to do with the periodic
boundary conditions, it is crucial that the long axis of the helix be
parallel to the z-axis of the periodic box. I know that XLeap reorients the
molecule in cartesian coordinate space when it creates the solvent box, but
I don't know how this reorientation works or how to modify it afterwards so
that the long axis of the helix ends up parallel to the z-axis. Does anyone
have any suggestions?

Thank you all in advance for your help.

Kenley Barrett

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