Bugfix 2 and 13 both address sleap, the 13th specifically regarding the
amoeba force field in proteins that have disulfide bonds in them. bugfix.2
was released in May of this year, so I would suggest that you recompile with
the bug fixes (cherry-picking patches is typically not recommended, since
each patch is created against the most recently-patched tree).
See
http://ambermd.org/bugfixesat.html and the v1.4 bug fixes.
Good luck,
Jason
On Fri, Dec 3, 2010 at 4:39 PM, Geoffrey Wood <gwood.mit.edu> wrote:
> Not since Feb of this year..... which is the bug in particular that is
> causing the problem?
>
>
>
>
> On Dec 3, 2010, at 4:17 PM, Jason Swails wrote:
>
> > 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.
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 - 14:00:07 PST
