Dear Amber users,
I have been calculated DNA-water interactions using hbond command in
ptraj. Since there is no description about the result in the amber
manual, could somebody explain me about:
1. What is the physical meaning of the value of lifetime and maxocc
2. Why does the value of lifetime increase twice when I define the time
value = 2.
Here is part of my script and its results
___________________________________________________________________
hbond series h1 distance 3.5 solventneighbor 6 solventdonor WAT O
solventacceptor WAT O H1 solventacceptor WAT O H2 out hbondc.dat
DONOR ACCEPTORH ACCEPTOR
atom#:res.atom atom#:res.atom atom#:res.atom %occupied distance angle
---------------- ---------------------------------
|663:22.O2P|solvent acceptor| 176.40 2.823 ( 0.23) 22.88 (13.94)
lifetime maxocc
-------------------------------------
4.9 ( 7.0) 61 |..........|
hbond series h1 time 2 distance 3.5 solventneighbor 6 solventdonor WAT O
solventacceptor WAT O H1 solventacceptor WAT O H2 out hbondc.dat
DONOR ACCEPTORH ACCEPTOR
atom# :res.atom atom# :res.atom atom# :res.atom %occupied distance angle
---------------- ---------------------------------
|663:22.O2P|solvent acceptor| 176.40 2.823 ( 0.23) 22.88 (13.94)
lifetime maxocc
-------------------------------------
9.9 ( 6.9) 61 |..........|
_____________________________________________________________________________
Best regards
Fajar
--
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> Fajar Rakhman Wibowo, M.Si.
> *
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Received on Wed Jan 14 2004 - 15:53:08 PST
