Dear AMBER Experts and Users,
I am trying to calculate native contacts for a nucleic acid over an MD
trajectory. Can someone please guide me how to specifically calculate the
"stem loop" contacts using cpptraj? What should be the appropriate "mask"
selection for this purpose?
Below is the reference script to calculate native contacts:
parm input.strip.parm7
trajin input.strip.nc
autoimage
nativecontacts name NC1 :1-47&!.H= \
writecontacts native-contacts.dat \
resout resout.dat \
distance 3.0 \
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
Any help would be much appreciated.
Best,
PN
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 10 2023 - 08:30:02 PDT
