Thank you all for your help. Apparently the problem was the top or the cdr
because when I change it the process run perfectly.
Thank you
Anthony
On Wednesday 06 July 2005 4:30 pm, David A. Case wrote:
> On Wed, Jul 06, 2005, Anthony Cruz wrote:
> > I try to run a minimization of a protein in water.
> > This is my .in:
> >
> > &cntrl
> > imin = 1,
> > maxcyc = 1000,
> > ncyc = 500,
> > ntb = 1,
> > ntr = 1,
> > cut = 10
> > /
> > Hold the Protein fixed
> > 500.0
> > RES 1 35
> > END
> > END
> >
> > When I try to run sander the job stops abruptly.
>
> It is required to have a title card before the &cntrl line. Since the
> title card could be blank, I can't tell if that is your problem or not.
>
> If not, look at the examples in the test cases (such as
> $AMBERHOME/test/dhfr/Run.dhfr.min), which is also a minimization of a
> protein in water. Try to figure out what is different between the test
> case and your example. (I am assuming that the test cases pass, since you
> didn't state otherwise.) Start with something that works, and slowly try
> to change it into the calculation you want.
>
> This is, of course, a general debugging strategy for all kinds of
> problems....
>
> ...dac
>
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Received on Thu Jul 07 2005 - 14:53:00 PDT
