if your structure is so bad that the energies aren't even printable
then you might try minimization in gas phase or perhaps GB before
adding water. that will just make it even more difficult.
have you looked at the atoms with GMAX? perhaps you can modify
them by hand first? Amber is not always graceful at dealing with
huge energies and very bad structures, especially in solution.
again, it is very hard to help since you haven't told us what you
are trying to do. making us read your output to see what is there
will not help you get more people to help you.
On 5/29/07, devrani mitra <devranimitra.gmail.com> wrote:
>
> Hello
>
> I'm attaching the output file for the details. Hope this simplifies the
> things.
>
> Thanks,
> Devrani
>
> On 5/29/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> > does your a_min_water.out file have any information in it?
> >
> > do the test cases pass?
> >
> > you need to give us much more information if you want help.
> >
> >
> > On 5/29/07, devrani mitra <devranimitra.gmail.com> wrote:
> > > Dear AMBER users,
> > >
> > > While running sander (for removing the bad contacts) following the
> > > tutorials, I'm getting the following error message:
> > >
> > > >> sander -O -i a_min.in -p a.parm7 -c a.crd -r a_min.rst -o
> > > a_min_water.out -ref a.rst
> > >
> > > p0_29153: p4_error: interrupt SIGSEGV: 11
> > >
> > > I'm not getting as which file do I need to correct. Please suggest.
> > >
> > > Thanks!
> > > Devrani
> > >
> > > Devrani Mitra, UC Davis
> > >
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> >
> >
> >
> >
>
>
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Received on Wed May 30 2007 - 06:07:31 PDT
