Dear AMBER Users and Experts,
I am trying to use the native contacts analysis script implemented in
CPPTRAJ for a couple of MD trajectories as follows:
parm input.strip.parm7
trajin combined.strip.nc <
http://combined.nc/>
nativecontacts name NC1 :1-85&!.H= \
writecontacts native-contacts.dat \
resout resout.dat \
distance 5.0 \
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
Here is an example for native.gnu 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 two sets of MD runs - wild-type protein and mutant protein. I used
the script above to calculate native.gnu files for these two systems.
I was looking to plot a "difference" plot for these two systems with the
hope that regions with the most significant differences would show up.
What is the correct way to go about this? If I take the difference of the
third column (normalized) for the wild-type and mutant cases, and try to
plot a contact map, is that it?
I would appreciate any help or guidance.
Thank you.
P.N.
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Received on Wed Jun 07 2023 - 12:00:02 PDT
