Hi,
On Tue, Aug 30, 2022 at 11:52 AM RIMJHIM MORAL via AMBER
<amber.ambermd.org> wrote:
> I am trying to calculate the lifetime of HBonds between two peptides using CPPTRAJ. As per the version I am using (Version V4.14.0) it is possible to calculate individually the lifetime for each hydrogen bonding pair. However, I am interested in calculating the average lifetime considering all the site-site combinations. The script I am running is given below:
If I understand what you're trying to do correctly, you want the
average over all hydrogen bonds? You could use the 'avg oversets'
analysis to calculate that; what that will give you is for every frame
you'll have a value from 0 to 1 (where 0 is no hydrogen bonds present
and 1 is all hydrogen bonds present). You can then run lifetime
analysis on that set with some cutoff (here I'm using 0.2 or 20% of
hydrogen bonds present but you may need to experiment), e.g.:
parm DPDP.parm7
trajin DPDP.nc
# Backbone hydrogen bonds
hbond BB out nbb.dat .N,H,C,O series uuseries bb.series.dat
run
# Average over all series sets
avg BB[solutehb] oversets name Avg out temp.dat
# Run lifetime analysis
lifetime Avg out temp1.dat window 10 cut 0.2
runanalysis
See the manual for full details. Hope this helps,
-Dan
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Received on Tue Aug 30 2022 - 11:30:03 PDT
