Re: [AMBER] Membrane protein tutorial

From: Jason Swails <>
Date: Tue, 10 Jun 2014 13:48:31 -0400

On Tue, 2014-06-10 at 13:03 -0400, Brian Radak wrote:
> But doesn't sander/pmemd adjust ifbox on-the-fly based on the lattice
> vectors in the restart file? I've seen this happen with triclinic boxes for
> example. I suppose the important thing is that ifbox > 0, which usually
> requires you to use solvateBox or solvateOct in tleap or else set box.

IFBOX never changes. It's a prmtop pointer (and sander/pmemd never
modifies the prmtop file).

I change it sometimes in ParmEd when deleting a periodic box (such as by
removing solvent and ions), but that's to make sure IFBOX is consistent
with what is expected by sander/pmemd... (Same thing with cpptraj --
"nobox" triggers a change in IFBOX when using "parmwrite")

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Jun 10 2014 - 11:00:04 PDT
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