Re: [AMBER] Obtaining contact maps with cpptraj

From: Alex Spasic <>
Date: Tue, 4 Dec 2018 15:25:22 -0500


skipnative option is very useful for me as well. Regarding the
nativecontacts command, I would suggest modifying the byresidue option. Now
it is summing contacts over all atom pairs in contact and based on that
calculates totalfraction and # contacts information. But if one atom pair
is in contact in all frames and another 10 atom pairs are in contact in
maybe 10% of frames then totalfraction will be small although the two
residues are really in contact the whole time. In my opinion, residue
contact information should be based on an atom pair that is in contact in
most of the frames.
Thanks for your great work on cpptraj.


On Mon, Dec 3, 2018 at 3:14 PM Daniel Roe <> wrote:

> Hi,
> 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.
> -Dan
> 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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> >
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Received on Tue Dec 04 2018 - 12:30:02 PST
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