AMBER Archive (2005)

Subject: Re: AMBER: sander problem

From: David A. Case (case_at_scripps.edu)
Date: Wed Jul 06 2005 - 17:30:59 CDT

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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