AMBER Archive (2009)

Subject: Re: [AMBER] Re: Error on equilibriation of Amber10

From: case (case_at_biomaps.rutgers.edu)
Date: Fri Jun 26 2009 - 07:17:42 CDT

On Fri, Jun 26, 2009, Masakazu SEKIJIMA wrote:
>
> I'm sorry for confusing you. I only wished to simplify my problem.
> These attached files (fkbp_wat.top and fkbp_wat_min.rst) are my real
> target system (protein and organic molecule surrounded by water and Cl-).
> I tried to equilibriate on your above advice again. Input file is md1.in
>
> But I did't execute sander well. After showing "fkbp_wat_1.out"'s message,
> it keep on stopping. So, I usually interrupt execution by ctrl^c.
> And, I can't get obtain details of error message.

I don't see what is wrong. I'd suggest this: start from the files in
$AMBERHOME/test/dhfr, which you know work ok. Try to see if you can slowly
morph that system (which works) into your system. Since minimization works,
a number of possible problems seem ruled out, but I don't recognize the
symptoms you report.

..dac
  

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