Dear all,
I have run the hbond analysis in cpptraj using AmberTools 13. As
specified in the manual of Amber14, the input syntax for lifetime
analysis should be something like this
lifetime [out <filename>] <dsetarg0> [ <dsetarg1> ... ] [window
<windowsize> [name <setname>]] [averageonly] [cumulative] [cut
<cutoff>] [greater | less]
Using this cue and from the amber mailing lists suggestions I wrote the input as
runanalysis lifetime H1[solutehb] out life.dat
In the reference manual it states:
[window <windowsize>] Size of window (in frames) over which to
calculate lifetimes/averages. If not specified lifetime/average will
be calculated over all sets
This understandable and I did not specify the window. My run
terminates in Error: Output file name specified but no window size
given ('window <N>')
If I specify the window size there is no error and I generate the
three files. the data in the files looks like this
#Frame LYS_211. LYS_211. LYS_211. LYS_211. LYS_211. TRP_249. TRP_249. TRP_249.
1 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
>From an earlier mail I received from Daniel, If the window is not
specified the output should look like this
#Set Nlifetimes MaxLT AvgLT TotFrames SetName
0 19 4 1.4211 27 GLU_13.O-VAL_2.N-H
Despite repeated efforts I am unable to get this output as when I dont
write the window size, the run terminates. Is there another keyword to
be added somewhere? Please share your experience, I am sure, I am not
doing something correct. My input without window looks like this
............................
trajin combined1-25.nc
hbond H1 series donormask
:178,211,249,251,252,253,281,
542,543,544,545,546,547.N*,H*,C*,O*
acceptormask :568.0 \
out hb5.dat dist 3.5 avgout avg5.dat
run
writedata solute.dat H1[solutehb]
runanalysis lifetime H1[solutehb] out life.5.dat
....................
Thank you once again to Daniel and others for being very helpful.
Regards
Ayesha Fatima
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Received on Sun Feb 22 2015 - 02:30:02 PST
