Hello,
On Tue, Sep 28, 2010 at 8:58 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
> Hello all
> I am using H-bondig facility for protein DNA complex.
> My script is as follows:
>
> trajin 1sa3_mono_prod1.mdcrd
> trajin 1sa3_mono_prod2.mdcrd
> donor mask :6.N7
> acceptor SER OG HG
> hbond distance 3.5 angle 120.0 nosort time 1.0 series hbond
>
> I am not getting any output file only getting
>
> PTRAJ: Successfully read in 4000 sets and processed 4000 sets.
> Dumping accumulated results (if any)
>
> HBOND SUMMARY:
> Data was saved to series hbond,
> data was not sorted, intra-residue interactions are NOT included,
> Distance cutoff is 3.50 angstroms, angle cutoff is 120.00 degrees
> Hydrogen bond information dumped for occupancies > 0.00
>
> 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
> | 166 :6.N7 | 2608 :145.HG 2607 :145.OG | 90.03 2.868 ( 0.15)
> 26.29 (13.75) 13.7 ( 18.7) 141
> |.....***......*..*.*o-******..****..*****.*.******|
> ---------------- ---------------------------------
> -------------------------------------
>
This right here is your summary, I believe. The key is listed above,
suggesting this is a fairly strong H-bond. There is no file that is dumped
out, the summary is printed straight to stdout.
Good luck!
Jason
>
> What is wrong here I am not getting.
> Should i got any output file or not?
> Waiting for suggestion
>
> With regard
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Sep 28 2010 - 07:30:06 PDT
