Re: [AMBER] how to use depreciated cpptraj code

From: Daniel Roe <>
Date: Tue, 3 Jan 2017 08:24:28 -0500


On Mon, Jan 2, 2017 at 2:21 PM, Chris Neale <> wrote:
> I do see that the cpptraj executable recommends to use the nativecontacts
> command. However, as far as I can tell this does not give minimum distances
> but, rather, the number of inter-group contacts within a specified cutoff.

As Hai mentioned, you should only need to add the 'mindist' keyword to
'nativecontacts', so e.g. this:

mindist :1 :7 out mindist.dat


nativecontacts :1 :7 mindist out mindist.dat

My reasoning for this was that since the 'nativecontacts' code can get
'mindist' and 'maxdist' essentially for free, the 'mindist' command
was redundant. I was just trying to avoid code duplication. However,
if there is a strong need for it I can easily add the command back (to
the GitHub version for now).

I'm usually wary about deprecating commands but 'mindist' hadn't been
around all that long (~6 months) so I thought maybe no one was using
it. Clearly I was wrong :-).


> Thank you,
> Chris.
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Tue Jan 03 2017 - 05:30:04 PST
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