Hi o ciao,
Google > Re: AMBER: PTRAJ: "hbond" analysis
Good luck (buona fortuna)
Giulio Rastelli wrote:
> 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.atom atom# :res.atom atom# :res.atom %occupied distance
> | 5800 :358.O1 | 1668 :105.H 1667 :105.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.N :105.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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Received on Tue Jun 14 2005 - 16:53:00 PDT
