Re: AMBER: error about using ambmask

From: Viktor Hornak <>
Date: Thu, 08 Dec 2005 08:53:22 -0500 wrote:

> I want to use "ambmask" to delete resnames out of 17A of resname TEM
> (nmuber is 467). I run it like the following:
> $AMBERHOME/exe/ambmask -p -c cyc_4_eq_com.crd.1 -prnlev
> 3 - out pdb -find :467 <:17

do you have "- out pdb" or "-out pdb"? The switch should not be
separated by space, i.e. it should be "-out".
In any case, even if that part is correct you may play a bit with
command line escapes, e.g. "<" in ":467 <:17" may be interpreted by the
shell rather than taken as literal input (as it should be). Start by
quoting the selection string, such as ':467 <:17', then try ':467
\<:17', etc. depending on your shell. If you're sure that the program is
getting the right input and still doesn't work, send me (out of list)
your topology and coordinate files and I'll have a look at them.

> the error message is
> DELETE error, unit -1073798496, file No such file or directory.
> How to solve this problem?
> ----------------------------------------------------------------------------
> --
> In addition, I wonder what is the name of this output file. In the
> amber8 manual, its default name is stdout. How to define my own filename?

Just redirect the output to a file, using ">" redirection (e.g. as in
cat file.txt > newfile.txt).


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Received on Thu Dec 08 2005 - 14:53:00 PST
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