AMBER Archive (2005)

Subject: AMBER: time and lifetime in hbond analysis (ptraj)

From: Giulio Rastelli (rastelli.giulio_at_unimo.it)
Date: Tue Jun 14 2005 - 09:23:50 CDT

Hi,
I am making a hbond analysis of selected atoms during a MD trajectory
using ptraj (amber8) using the input below. First, I am not sure about
the meaning of the "time" keyword in the hbond command (sometimes I saw
values of 1 or 0.75). If I'm correct there is no clue in the manual.

Output:

atom# :res_at_atom atom# :res_at_atom atom# :res_at_atom %occupied distance
| 5800 :358_at_O1 | 1668 :105_at_H 1667 :105_at_N | 99.50 3.023 ( 0.13)

angle lifetime maxocc
19.90 (11.37) 180.9 (150.9) 488 |@@@@@@@@@@|

Over a trajectory of 400ps, with 400 snapshots collected, would this
output mean that the hbond has 99.5% occupancy during the trajectory,
a distance of 3.023+/-0.13, an angle of 19.9+/-11.37 (I assume that
the number in parentheses are the standard deviations, right?)
Then, how are the lifetime and maxoccupancy defined?

Input:

trajin test_mmd.xyz
center :163
rms first @CA,N,C
prnlev 3
donor mask @O1
acceptor mask :105_at_N :105_at_H
hbond series hbond out test_hbond.out \
    solventdonor WAT O \
    solventacceptor WAT O H1 \
    solventacceptor WAT O H2 \
    time 1.0 distance 3.5

Thanks very much for the info
Giulio Rastelli 

-- 

Prof. Giulio Rastelli
Dipartimento di Scienze Farmaceutiche
Facolta' di Bioscienze e Biotecnologie
Universita' di Modena e Reggio Emilia
Via Campi 183
41100 Modena - ITALY
-------------------------------------
tel 0039-059-2055145
fax 0039-059-2055131
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