AMBER Archive (2007)

Subject: Re: AMBER: Could not find cntrl namelist

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Mon Jul 09 2007 - 16:31:18 CDT

Unfortunately I am unfamiliar with with "od -c" (octal dump as chars)". Also, I
use nano or vim, don't know emacs.

As to the out file, it was not cut/pasted, it was scp sent from the computing
machine to the desktop, and on this directly attached to the gnome email.

francesco

--- Thomas Cheatham III <tec3_at_utah.edu> wrote:

>
> > No blank line before the one starting with #, and formatting was exactly as
> in
> > tutorial 1B. Now corrected by adding a comma after 300.0 (I find this
> curious
> > because I was able to run that tutorial 1B).
> >
> > On trying to run sander, same error. Attached is the out file. Of course
> the
> > mdcrd file was not generated.
>
> Looking at this output file with "od -c" (octal dump as chars) shows that
> in the mdin file are characters 302 and 240 at the start of each line. In
> my emacs view of the file, it looks like a A with a hat (^) character
> (similar to the character for Angstroms). Perhaps your cut and paste is
> adding spurious characters. I would edit the "mdin" file to remove these
> spurious characters...
>
> -- tec3
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