Yet more advice:
try using pmemd instead of sander. They give the same results for what
pmemd does, but pmemd typically has better error-checking.
HTH,
Jason
On Thu, Aug 11, 2011 at 12:06 PM, M. L. Dodson <mldodson.comcast.net> wrote:
>
> On Aug 11, 2011, at 10:56 AM, case wrote:
>
> > On Thu, Aug 11, 2011, Nyla Zaman wrote:
> >>
> >>
> >> -------------------------------------------------------
> >> Amber 10 SANDER 2008
> >> -------------------------------------------------------
> >>
> >
> > Do the sander test cases run correctly? If so, try to take one of those
> > inputs (e.g. in $AMBERHOME/test/dhfr), convert it to your system, and
> slowly
> > try to morph the inputs that work into yours.
> >
> > If the test cases don't run, then you need to re-examine how you
> installed
> > Amber.
> >
> > ....dac
> >
>
>
> Another possibility is that two atoms are so close their VDW energy
> calculation causes floating point overflow.
>
> This is the symptom I ran into when trying to run minimizations with
> packmol-
> created starting PDB files: the output above, then sander just hung without
> any further output.
>
> In this case, nothing was wrong with sander and nothing was wrong with the
> input
> file. It was the starting structure that was at fault. To diagnose this,
> try
> running a single step and see if it completes with high energies (VDW or,
> maybe,
> electrostatics.)
>
> Bud Dodson
> --
> M. L. Dodson
> Business email: activesitedynamics-at-gmail-dot-com
> Personal email: mldodson-at-comcast-dot-net
> Gmail: mlesterdodson-at-gmail-dot-com
> Phone: eight_three_two-five_63-386_one
>
>
>
>
>
>
>
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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 Thu Aug 11 2011 - 10:00:02 PDT
