[AMBER] [cpptraj] Problem with nativecontacts

From: Juan Eiros Zamora <j.eiros-zamora14.imperial.ac.uk>
Date: Wed, 28 Jan 2015 13:02:10 +0000

Dear all,

I am working with a protein that has three separate subunits, and I am
trying to generate a 'heat map' of the interactions between these
subunits. What I intend to do is monitor the distance between residues
in two of the subunits through time, and each time the distance goes
below a certain value (<5.4 A for example) register it. Then I want to
obtain a graph with the frequency of this contacts between each pair of
residues (1 being contact through the entire simulation and 0 no contact
at any point during the simulation).

For this I have been trying to use the nativecontacts command in
cpptraj. Nevertheless I am not obtaining satisfactory results because I
am not sure that this command is exactly fitted for my purposes.

In particular, I am specifying as <mask2> the CA of one of the subunits
(:1-161.CA), and <mask1> as the CA of the other subunit I am interested
in (:249-458.CA). I am also enabling the results to be written as a
contacts map in 2D with the map flag. Nevertheless, the results I am
getting from this map file are not normalised from 0 to 1, and the
interactions are recorded between from :1 to :458, thus obtaining a
symmetrical map.

Has anyone encountered these problems before? Any suggestions on how to
tackle this matter would be of great help. I am also attaching an image
showing the results I get from the map file.

My cpptraj.in file looks like this:

parm nowatcompletehow.prmtop
trajin 05_Prod_000-050ns_completehow_nowat.nc
trajin 05_Prod_050-100ns_completehow_nowat.nc
trajin 05_Prod_100-150ns_completehow_nowat.nc
trajin 05_Prod_150-200ns_completehow_nowat.nc
trajin 05_Prod_200-250ns_completehow_nowat.nc
trajin 05_Prod_250-350ns_completehow_nowat.nc
trajin 05_Prod_350-450ns_completehow_nowat.nc
trajin 05_Prod_450-500ns_completehow_nowat.nc
average avg.nc
reference avg.nc [ref1]
nativecontacts :249-458.CA :1-161.CA distance 5.4 ref [ref1] byresidue
map mapout map2.dat

Thanks in advance,

Juan Eiros

AMBER mailing list

(image/png attachment: map2.png)

Received on Wed Jan 28 2015 - 05:30:06 PST
Custom Search