Dear Daniel and all people using Amber,
I finally managed to get what I wanted with the hbond analysis. but
now how do I interpret my data. In my complex, I observe that my
ligand has an oxygen that behaves as an acceptor. This I observed from
the general no series avgout data. in case of time series without
specifying any acceptor or donor, I cannot see data pertaining to my
ligand however, i specified it in the acceptor mask and now I see t
appears in the data set. when I run the life time series, i get the
three files with most of the frames showing zero value except in one
or two frames, somewhere I can see the figure 2. In the header in the
life.dat, I see only my ligand name and frame. what does the ligand
residue name specify. If it specifies the residue forming the hbond,
which is the residue it is forming with? I looked at the AmberTools13
information on lifetime but I am still blur on it.
Please share your experience in this regard. I shall be grateful
Regards
Ayesha Fatima
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Received on Fri Feb 20 2015 - 06:00:06 PST
