[AMBER-Developers] sleap / tleap box type confusion?

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 22 Feb 2010 15:55:41 -0500


I'm not sure if what I'm seeing with sleap/tleap is supposed to be
happening or not...

When I run the following script:
source leaprc.ff99SB
l = loadpdb GM2.pdb
addIons l Na+ 0
solvateOct l TIP3PBOX 15.0
saveAmberParm l prmtop inpcrd


through sleap, ifbox in the prmtop is set to 1.

through tleap, ifbox in the prmtop is set to 2.

When I run this with NVT (sander or pmemd), the box in sleap gets
squished into a shape that is definitely not octahedral (iwrap=1).
When I use the prmtop generated by tleap, the box keeps its octahedral
shape. When I use the sleap-generated prmtop but change ifbox from 1
to 2, it keeps its shape.

Is this a bug, or a feature? Is it documented somewhere? Is there any
way to change this?


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER-Developers mailing list
Received on Mon Feb 22 2010 - 13:00:05 PST
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