It looks to me that no atoms were selected as acceptor. Can you try to use
"mask" to define acceptor?
Use
acceptor mask :4GA.O2 :4GA.H20
instead of
acceptor 4GA O2 H20
This could be a bug in the ptraj, and we will take a look.
Thanks for bringing this up and if you can not fix the problem, feel free to
let me know.
Jianyin
On 1/3/07, nag raj <nagaraju_chem.yahoo.co.in> wrote:
>
> Dear Amber users,
> I am trying to analyse hydrogen
> bonds using ptraj (AMBER8), I am not getting values
> any suggestion is appreciated. Here is my ptraj
> script file.
> # H-bond analysis in cyclodextrine molecule
> #
> trajin b1_lg2_hb_con2_md_run2.crd 1 40 1
>
> #-- Donors from beta cyclodextrine
> donor mask :1-7.O2
> donor mask :1-7.O3
> donor mask :1-7.O4
> donor mask :1-7.O5
> donor mask :1-7.O6
>
> #-- Acceptors from beta cyclodextrine
> acceptor 4GA O2 H20
> acceptor 4GA O3 H30
> acceptor 4GA O6 H60
> hbond distance 3.6 angle 160 print .05 series out
> zzzz.out
>
> Here I attached the out put file,
>
> 4GA 4GA 4GA 4GA 4GA 4GA 4GA L2H WAT WAT
> WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
> ...
> PTRAJ: donor mask :1-7.O6
> Mask [:1-7.O6] represents 7 atoms
>
> PTRAJ: acceptor 4GA O2 H20
>
> PTRAJ: acceptor 4GA O3 H30
>
> PTRAJ: acceptor 4GA O6 H60
>
>
> Processing AMBER trajectory file
> b1_lg2_hb_con2_md_run2.crd
>
> Set 1 ........................................
>
> PTRAJ: Successfully read in 40 sets and processed 40
> sets.
> Dumping accumulated results (if any)
>
> HBOND SUMMARY:
> Data was saved to series out,
> data was sorted, intra-residue interactions are
> NOT included,
> Distance cutoff is 3.60 angstroms, angle cutoff
> is 160.00 degrees
> Hydrogen bond information dumped for occupancies
> > 0.05
>
> 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
>
> DONOR ACCEPTORH ACCEPTOR
> atom# :res.atom atom# :res.atom atom# :res.atom
> %occupied distance angle lifetime maxocc
>
>
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Received on Sun Jan 07 2007 - 06:07:27 PST
