Re: [AMBER] Obtaining contact maps with cpptraj

From: Daniel Roe <>
Date: Mon, 3 Dec 2018 15:14:13 -0500


Sorry for the long delay on replying here. I seem to be falling
farther and farther behind on answering mail these days...

I've added a new keyword to the 'nativecontacts' command in the GitHub
version of cpptraj: 'skipnative' (PR here: This skips the initial
native contacts determination, so all contacts found are considered
non-native. It's not super polished and I've only done limited testing
so far, but I think it should get you the data that you want. Any/all
feedback is welcome.


On Thu, Nov 22, 2018 at 11:48 PM Stefan Ivanov <> wrote:
> Dear Amber users,
> I need by-residue contact maps from an MD trajectory. I know that the nativecontacts command provides this functionality; however, the maps are divided into "native" and "nonnative" with respect to a reference structure or the first frame in the trajectory. I need a map of all contacts, without such a split, which in my case is artificial and meaningless. Is there a way to obtain a map of all contacts, a combination of "native" and "nonnative" contacts, preferably with a timeseries file as well? It occurred to me to increase the cutoff, so all contacts would be "native," but trajectory processing is too slow.
> Sincerely,
> Stefan
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Received on Mon Dec 03 2018 - 12:30:02 PST
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