Dear AMBER users,
I'm sorry if this question has been answered elsewhere.
I'm trying to understand the schematic that the latest version of ptraj
gives in its hydrogen bonding facility:
I understand that this is the key for what the symbols mean:
* Dumping schematic of time series after each h-bond, key follows:
| . - o x * @ |
0-5% 5-20% 20-40% 40-60% 60-80% 80-95% 95-100% occupancy*
My question is: %occupancy of what? I've used the H-bonding facility to
analyze trajectories both 100ns and 20ns long, and both times I've seen a
string of 50 symbols to the right of the output table. What would one string
represent? For example:
*| ..-.o.- .---. o.. o..................x *..@@o@|*
What does it mean to say that, for each ".", the H-bond is 95-100% occupied
for 1/50 of the trajectory? Does this mean, if I specified my cutoff
distance as 4 and my angle as 179, that the Hbond form at 1/50 of the
trajectory was at least (0.95)*4 = 3.8 Å in length and at an angle of at
least 179.95º?
Thank you all in advance,
--
Kamali Sripathi
Graduate Student, Medicinal Chemistry
Walter Laboratory
930 North University
Ann Arbor, MI, 48109
ksripath.umich.edu
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Received on Thu May 05 2011 - 14:30:02 PDT
