AMBER Archive (2004)

Subject: RE: AMBER: md.out & plot

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Nov 23 2004 - 16:59:58 CST

The summary files are just text files... What do you mean by excel can't
recognise these files?

Go to import data -> select the file and choose space delimited and you
should get two columns imported, one with the time (that can easily delete)
and one with the data.

The only problem you come across is with differences between UNIX and DOS
text formating. In which case on Linux you can use the command unix2dos to
convert the format (or 'tr').

unix2dos mytextfile.txt

Alternatively if you just simply want to remove the time column from the
text file do:

cat file.txt | awk '{print$2}' > column2.txt

This will give you simply column two of the text file.

All the best
Ross

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|\oss Walker

| Department of Molecular Biology TPC15 |
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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of bybaker_at_itsa.ucsf.edu
> Sent: 23 November 2004 14:24
> To: amber_at_scripps.edu
> Subject: AMBER: md.out & plot
>
> Hello, Amber:
>
> I use the command of 'perl process_mdout.perl md1.out' to generate the
> summaries from one Amber md run. I would like to plot them
> with Excel or
> Prism programs. The files' format can not be recognized by either of
> these programs. I don't have 'xmgr'. If I manually delete the time
> points, it takes a long time and easy to make mistakes. Can any one
> suggest me how to convert these files into the files that can
> be used for
> Excel?
>
> Thank you very much for your help.
>
> Regards
>
> Bo
>
>
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