Re: Help! Sander run error: Bus error

From: David Case <>
Date: Mon 15 Apr 2002 22:32:16 -0700

On Thu, May 02, 2002, William Wei wrote:
> Hi, Amber experts:
> Following your idea, fortunately I got Amber 7 package today. So I compiled
> it. Still I got the "Bus error" message while I run sander to minimize my
> structure.

You will probably need to get a better starting structure, since your
starting energy is 10**11. Here are some thoughts.

(1) just try a short protein-only minimization before solvating.

(2) always set ntpr =1 when you are having troubles at the very beginning.

Even so, you shouldn't get a bus error....if you want, you could send
your input files, along with info about yoru MACHINE file and hardware
configuration. If we can reproduce the problem, we can hope to track
it down. Or, you could try using a debugger yourself, if you know how
that is done.

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Mon Apr 15 2002 - 22:32:16 PDT
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