AMBER Archive (2009)

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

From: Masakazu SEKIJIMA (sekijima_at_gsic.titech.ac.jp)
Date: Thu Jun 25 2009 - 12:41:39 CDT

2009/6/25 case <case_at_biomaps.rutgers.edu>:
> I am confused: in the files you posted (most of which are irrelevant), you
> didn't have the above input file. Instead, you had a "test.csh" script, which
> used a "test.in" input that was not the one you list above, and which set
> irest=1, which would be wrong for an initial minimization. So, did you
> actually use the script above?
>
> The above script might fail because you are trying to do constant pressure
> simulation starting from zero K. You need to equilibrate to near room temp.
> at constant volume *before* turning on constant pressure.

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.

> Also, is there a queuing system involved here? You may be losing error
> messages somewhere. Also, when you are seeing problems like this, look
> in more detail, by setting ntpr=1 (and nstlim to 10 or so).

Yours Sincerely, 

-- 
_____
SEKIJIMA Masakazu, Ph.D.
Mail: sekijima_at_gsic.titech.ac.jp
  • application/octet-stream attachment: md1.in
  • application/x-csh attachment: test.csh

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