Re: [AMBER] CPPTRAJ average residue-wise contact map

From: Daniel Roe <>
Date: Thu, 2 May 2019 08:25:25 -0400


You can get a combined contacts map by just considering every contact
to be "non-native" using the 'skipnative' keyword; this keyword is
relatively new so use the GitHub version of cpptraj.

Normalizing it to 1 is a little more problematic. The way cpptraj
normalizes by-residue contacts is a little strange - the final values
currently reflect how many potential contacts a residue can make (so
e.g. TRP residues can end up with higher values than GLY residues). To
do a 1 to 1 map you could either to a C-alpha contacts map (while
increasing the default distance cutoff), or create a pseudo trajectory
of each side chain center of mass (via 'vector' and 'writedata
vectraj'), then dot he native contacts analysis on the pseudo
trajectory (more details in the manual). Let me know if you have more

Hope this helps,


On Wed, May 1, 2019 at 3:06 PM anu chandra <> wrote:
> Hello Amber users,
> I am trying to generate an average residue-wise contact map along the
> simulation time. Using nativecontacts in CPPTRAJ, I could generate native
> and nonnative contact map as well as residue time series contact. However,
> I wonder whether it is possible to get an average residue-wise contact map
> matrix (where 1 for contact and 0 for no contact), using CPPTARJ, that
> contain sum of both native and nonnative contacts?
> Any help would be appreciated.
> Best regards
> Anu
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Received on Thu May 02 2019 - 05:30:01 PDT
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