AMBER Archive (2008)

Subject: RE: AMBER: Conversion between truncated octahedron and orthorohombic box

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Oct 26 2008 - 11:56:50 CDT

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,

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
#NGUYEN CONG TRI#
Sent: Saturday, October 25, 2008 7:37 PM
To: amber_at_scripps.edu
Subject: AMBER: Conversion between truncated octahedron and orthorohombic
box

 

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,

Tri

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