Hi,
I am trying to use the native contacts analysis script implemented in
CPPTRAJ as follows:
*Without specifying a reference*
parm step3_input.strip.parm7
trajin combined.nc
nativecontacts name NC1 :1-67&!.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
lifetime NC1[NC] out lifetime.dat
run
*By specifying a reference*
parm step3_input.strip.parm7
trajin combined.nc
reference ../step3_input.pdb
nativecontacts name NC1 :1-67&!.H= \
byresidue out nc.all.res.dat mindist maxdist \
distance 3.0 reference map mapout resmap.gnu \
contactpdb native-contacts.pdb \
series seriesout native.dat
run
My question is: what do the columns in lifetime.dat, native.gnu,
nonnative.gnu represent? I understand the residue indices in these files
but do not understand the fractional values reported. Here is an example
for native.gnu:
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
and for nonnative.gnu:
1.000 1.000 0.0000
1.000 2.000 8.8826
1.000 3.000 0.9303
1.000 4.000 0.1229
1.000 5.000 0.0129
1.000 6.000 0.0060
1.000 7.000 0.0102
1.000 8.000 0.0004
1.000 9.000 0.0029
1.000 10.000 0.0012
1.000 11.000 0.0053
1.000 12.000 0.0024
1.000 13.000 0.0787
What does the third column represent in these files?
Thank you for your help and guidance!
P.N.
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Received on Tue Jan 03 2023 - 11:30:02 PST
