Dear Daniel,
Thank you for your quick response. About my "series" keyword. I did
not change anything in the input file except that previously I was not
specifying the donors and acceptors. I am attaching my output files.
hbond3.out file is the one with series no acceptors or donors
specified. avg3.zip is the corresponding avgout file. if we search for
the residue 568, it cannot be found. However, without the keyword
series as given in hbond2.out file and the corresponding avg2.out, the
residue keyword search reveals it to be there. Now in the latest input
file which is as follows
.....
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
.......................
there the keyword series is defined as well as the acceptor and donor
masks and my output shows all the data relevant to these specified
residues
About the lifetime run, I am attaching my output life-rev.zip which is
unlike the one that you have sent since I specified window number. If
I run without the window number as given in the input above, I get the
"Error: no window number specified" which can be seen in the
hbond3.out file. This is consistent with the command line in the
manual which says that the windows <number> should be specified. So
where am I going wrong still? If the output is like the one you have
pasted, the answer is still interpretable and self explanatory. I am
attaching my output files for reference. Also about the figure 2, very
sorry, it is actually number 2 that is appearing in some columns of
the life-rev.zip files
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Received on Sat Feb 21 2015 - 09:00:02 PST
