RE: AMBER: Conversion between truncated octahedron and orthorohombic box

From: Ross Walker <>
Date: Sun, 26 Oct 2008 09:56:50 -0700

Hi Tri,


I've never actually tried this but one approach I could imagine might work
would be to convert the prmtop and restart file to a pdb, containing the
water, then load this into xleap and use solvatebox to solvate your
truncated octahedron, using a small buff or say 1.0 should mean just the
corners get solvate although you might have to play with things a bit.


You'd then just need to do a short equilibration to let the density
stabilize and get things back up to the correct temperature.


Good luck,



From: [] On Behalf Of
Sent: Saturday, October 25, 2008 7:37 PM
Subject: AMBER: Conversion between truncated octahedron and orthorohombic


Dear all,


I pre-equilibrated my system in Amber in a very long simulation. To reduce
the box size I used a truncated octahedron box. I'd like to use that
equilibrated structure for a QM/MM simulation with Gromos Interface. So I
have to convert the coordinate and topology into Gromos format. But I wasn't
aware that only orthrhombic box is allowed.


Is there anyway to convert the truncated octahedron into orthorhombic
symmetry without having to equilbrate my system again?


Thank you for any sugguestion.


Best regards,


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
Received on Mon Oct 27 2008 - 05:07:37 PDT
Custom Search