Have you applied all of the bug fixes?
On Fri, Dec 3, 2010 at 4:12 PM, Geoffrey Wood <gwood.mit.edu> wrote:
> 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
>
> i.e.:
>
> sleap
> 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:
>
> REMARK
> 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
> TER
>
>
>
> Any ideas about what is happening?
>
> Thanks in advance.
>
>
>
>
>
>
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Dec 03 2010 - 13:30:05 PST
