Re: [AMBER] Proper output form of DCCM Analysis using ptraj

From: Jason Swails <>
Date: Wed, 21 Jan 2015 07:41:19 -0500

On Wed, 2015-01-21 at 09:31 +0530, Suchetana Gupta wrote:
> Hi Dan
> Thanks for the suggestions. I tried using small residue selections and they
> are working fine in Amber12. But the moment I increase the number of
> residues, the output file doesn't contain the data in the correct matrix
> format. I am sure I am getting 120x120 values, but the output is not in a
> matrix format. I am attaching a screenshot if it helps.
> Any help would be appreciated.

You solved the problem exporting it to a spreadsheet-style format, but
I'll just point out what was happening here. The editor you were using
was employing "wrapping" -- that is, 120 numbers did not fit on a single
line, so it "wrapped" those that wouldn't fit to the next line on the
screen (but *not* the next line in the actual file). If you use the
left and down arrows in an editor like vi or emacs, you can tell where
one line stops and the next starts.

Most editors give you the option to turn *off* wrapping (so the file
scrolls left-and-right as well as up-and-down). Just google your editor
and "turn off wrapping" to look for instructions.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Jan 21 2015 - 05:00:03 PST
Custom Search