Dear All,
I'm interested in calculating the contacts between the interface residues of the protein-protein interaction. I used the nativecontacts command in the ambertools.
This is how my script looks:
trajin pH.nc 1 10000 10
autoimage
strip :WAT
reference min.rst7
nativecontacts :501-504,535,546,549,550,570,573,574,576-585,586,733,872-874,957,959 writecontacts nativecontacts.dat resout res noimage distance 7.0 out contacts.out first resoffset 2 contactpdb contacts.pdb byresidue map mapout gnu series seriesout nativeseries.dat
This is how the output file looks:
set size square
set pm3d map corners2color c1
set xlabel "Residue"
set ylabel "Residue"
set yrange [ 500.000: 961.000]
set xrange [ 500.000: 961.000]
splot "-" with pm3d title "native.gnu"
501.000 501.000 0.0000
501.000 502.000 0.0000
501.000 503.000 0.0000
501.000 504.000 0.7000
501.000 505.000 0.0000
501.000 506.000 0.0000
501.000 507.000 0.0000
501.000 508.000 0.0000
501.000 509.000 0.0000
501.000 510.000 0.0000
501.000 511.000 0.0000
501.000 512.000 0.0000
501.000 513.000 0.0000
501.000 514.000 0.0000
501.000 515.000 0.0000
501.000 516.000 0.0000
501.000 517.000 0.0000
501.000 518.000 0.0000
501.000 519.000 0.0000
501.000 520.000 0.0000
501.000 521.000 0.0000
501.000 522.000 0.0000
501.000 523.000 0.0000
501.000 524.000 0.0000
501.000 525.000 0.0000
501.000 526.000 0.0000
501.000 527.000 0.0000
....
I'm only interested in seeing the contacts for the atoms in the masks. Is there a way to just print the contacts for the residues in the mask1 to the residues in the mask2??
Looking forward to the suggestion.
Thank you,
Regards
Sowmya
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Received on Thu Apr 19 2018 - 09:30:02 PDT
