[AMBER] amoeba waters

From: Geoffrey Wood <gwood.MIT.EDU>
Date: Fri, 3 Dec 2010 16:12:48 -0500

Dear Amber users,

I wanted to do something fairly simple, that is set up a box of amoeba waters using sleap.

1. If I run the tests in the ~/amber11/test/sleap/amoeba directory (Run.amoeba Run.amoeba_sol) then they pass.

2. If I try and solvate one water molecule loaded from a pdb file (see below) then I get a "segmentation fault" when I try to save the param file


set default echo on
source leaprc.amoeba
loadoff amoeba_wat.off
A = loadpdb wat.pdb
solvateoct A WATBOX 4.0
savepdb A amoebaWat.pdb
saveamoebaparm A amoebaWat.prmtop amoebaWat.xyz

--> Segmentation fault

my Pdb file just looks like:

ATOM 1 O WAT 1 0.782 0.902 1.871
ATOM 2 H1 WAT 1 0.782 0.902 2.828
ATOM 3 H2 WAT 1 1.564 1.353 1.552

Any ideas about what is happening?

Thanks in advance.

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Received on Fri Dec 03 2010 - 13:30:04 PST
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