AMBER Archive (2003)

Subject: AMBER: lifetime in ptraj hbond

From: Fajar Rakhman Wibowo (Fajar.Wibowo_at_uibk.ac.at)
Date: Fri Dec 12 2003 - 03:28:45 CST

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_at_atom atom#:res_at_atom atom#:res_at_atom %occupied distance angle
---------------- ---------------------------------
|663:22_at_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_at_atom atom# :res_at_atom atom# :res_at_atom %occupied distance angle
               ---------------- ---------------------------------
|663:22_at_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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