Try running the files with igb=1 using pmemd instead of sander. pmemd
tends to catch errors better.
Good luck,
Jason
On Wed, Jan 18, 2012 at 9:41 AM, Baptiste Legrand <bap.legrand.gmail.com>wrote:
> Thanks Jason for your answer. I tested removing the &ewald namelist and
> setting igb=6 or igb=1 but I have the same issue. As it was a bit tricky
> for me to prepare the inpcrd and prmtop homotrimer files, my objective
> was to quickly tested them on a simple minimization. I finally hope to
> launch a simulation on this complex in a solvent box. May be, it will
> work directly with the box.
>
> Best regards,
> Baptiste
>
> The objective is finally to launch a simulation in a solvent box.
>
> Le 18/01/2012 15:08, Jason Swails a écrit :
> > What happens when you remove the&ewald namelist completely and set igb=6
> > instead? If that fixes it, do you really the distance-dependent
> > dielectric? Can you use a Generalized Born implicit solvent method
> instead
> > (or just vacuum, if handled with care)? I don't think that option is
> > frequently tested since it's an unusual choice, especially when GB
> options
> > are available and do a much better job at calculating solvation effects.
> >
> > HTH,
> > Jason
> >
> > On Wed, Jan 18, 2012 at 6:22 AM, Baptiste Legrand<bap.legrand.gmail.com
> >wrote:
> >
> >> Dear all,
> >>
> >> I'm trying to minimize a homotrimer of small coupounds in vacuum with
> >> amber10 but it fails. the out file have only these lines:
> >> ------------------------------**-------------------------
> >> Amber 10 SANDER 2008
> >> ------------------------------**-------------------------
> >> and the processor continue to work at full charge (99%).
> >>
> >> I used antechamber to create a prepin file and then a frcmod for the
> >> monomer and I have any problem to launch a minimization step. So,
> starting
> >> from these files, I created new prmtop and inpcrd files for a trimer
> using
> >> xleap (I joined these files and the min.in script). On a display, the
> >> complex is fine nevertheless the minimization fails.
> >> Thanks in advance.
> >>
> >> Best regards,
> >> Baptiste
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jan 18 2012 - 08:00:02 PST
