Dear AMBER Users and Experts,
I am trying to use the native contacts analysis script implemented in
CPPTRAJ as following:
parm input.strip.parm7
trajin combined.strip.nc <
http://combined.nc/>
nativecontacts name NC1 :1-110&!.H= \
writecontacts native-contacts.dat \
resout resout.dat \
distance 4.0 \
byresidue out all-residues.dat mindist maxdist \
map mapout gnu \
contactpdb contactspdb.pdb \
series seriesout native-contacts-series.dat
run
Below is an example of native.gnu output file:
1.000 1.000 0.0000
1.000 2.000 16.6333
1.000 3.000 0.0000
1.000 4.000 0.0000
1.000 5.000 0.0000
1.000 6.000 0.0000
1.000 7.000 0.0000
1.000 8.000 0.0000
1.000 9.000 0.0000
1.000 10.000 0.0000
I have a couple of questions regarding this:
1. What does the third column in the above output represent? Is it a
normalized frequency of contacts in percentage?
2. I have two replicates of the same system. I generated output files for
both runs using the same reference structure in the above format. I want to
show the difference between the fraction of native contacts for the two
runs and identify the regions/residues that show a difference. Does
subtracting the third column (for each run) and plotting a contact map make
sense?
I would appreciate any help/guidance regarding this.
Best regards,
-PN
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Received on Wed Mar 27 2024 - 16:30:02 PDT
