Dear Daniel
I tried cpptraj but following error occurred :
Error: Could not set up file prod_1-8.binpos for reading.
Error: trajin: Could not set up trajectory.
Then again i used ptraj and it worked for me this time.. my output is as
under:
HBOND SUMMARY:
Data was saved to series hydrogen3, output to file output_hb3.dat,
data was sorted, intra-residue interactions are NOT included,
Distance cutoff is 5.00 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
| 3029 :198.N | 3030 :198.H 5852 :374.N2 | 76.16 3.692 ( 0.24)
45.93 ( 8.91) 4.7 ( 5.5) 59
|xxxxxxxx*x*xxxx*xx***xxooxx*xxxx*x*x*xxx*x*xxx****|
| 2991 :196.N | 2992 :196.H 5851 :374.N1 | 10.67 4.701 ( 0.22)
53.65 ( 5.08) 1.5 ( 1.2) 18 |.-........ ...-o-.... --- .
..- ... . |
| 2991 :196.N | 2992 :196.H 5851 :374.N1 | 10.67 4.701 ( 0.22)
53.65 ( 5.08) 1.5 ( 1.2) 18 |.-........ ...-o-.... --- .
..- ... . |
| 2987 :195.OG1 | 2988 :195.HG1 5856 :374.O4 | 8.84 4.100 ( 0.55)
41.02 (13.96) 1.8 ( 1.5) 13 |-... .. . ....oo--.-. .
.. .. |
| 3029 :198.N | 3030 :198.H 5853 :374.O1 | 3.52 4.650 ( 0.25)
56.35 ( 2.97) 1.1 ( 0.4) 4 |. . . .. ...
. |
| 2981 :195.CB | 2988 :195.HG1 5856 :374.O4 | 3.24 4.278 ( 0.28)
49.82 ( 8.94) 1.6 ( 1.1) 9 |.
.---... |
| 2987 :195.OG1 | 2988 :195.HG1 5851 :374.N1 | 2.96 4.436 ( 0.31)
51.60 ( 8.01) 1.3 ( 0.6) 4 | . .. . ......
..- |
| 2982 :195.HB | 2988 :195.HG1 5856 :374.O4 | 1.41 4.569 ( 0.26)
50.54 ( 7.77) 1.4 ( 0.8) 6 |
-... |
| 2981 :195.CB | 2988 :195.HG1 5851 :374.N1 | 0.54 4.833 ( 0.14)
37.52 (15.03) 1.3 ( 0.8) 4
| |
| 2983 :195.CG2 | 2988 :195.HG1 5851 :374.N1 | 0.18 4.840 ( 0.11)
47.12 ( 6.50) 1.0 ( 0.0) 1
| |
| 2985 :195.HG22| 2988 :195.HG1 5851 :374.N1 | 0.12 4.786 ( 0.17)
52.01 ( 5.55) 1.0 ( 0.0) 1
| |
| 2984 :195.HG21| 2988 :195.HG1 5851 :374.N1 | 0.09 4.826 ( 0.18)
54.28 ( 2.63) 1.2 ( 0.4) 2
| |
| 2986 :195.HG23| 2988 :195.HG1 5851 :374.N1 | 0.07 4.808 ( 0.14)
52.99 ( 4.03) 1.0 ( 0.0) 1
| |
| 2983 :195.CG2 | 2988 :195.HG1 5856 :374.O4 | 0.06 4.225 ( 0.29)
53.08 ( 5.44) 1.0 ( 0.0) 1
| |
| 2985 :195.HG22| 2988 :195.HG1 5856 :374.O4 | 0.04 4.586 ( 0.18)
53.17 ( 5.62) 1.0 ( 0.0) 1
| |
| 2989 :195.C | 2992 :196.H 5851 :374.N1 | 0.04 4.921 ( 0.07)
47.38 (12.26) 1.2 ( 0.4) 2
| |
| 2989 :195.C | 2992 :196.H 5851 :374.N1 | 0.04 4.921 ( 0.07)
47.38 (12.26) 1.2 ( 0.4) 2
| |
| 2984 :195.HG21| 2988 :195.HG1 5856 :374.O4 | 0.04 4.719 ( 0.24)
56.23 ( 2.64) 1.0 ( 0.0) 1
| |
| 2991 :196.N | 2988 :195.HG1 5851 :374.N1 | 0.03 4.853 ( 0.06)
50.20 ( 6.16) 1.0 ( 0.0) 1
| |
| 3009 :196.O | 2988 :195.HG1 5856 :374.O4 | 0.02 4.671 ( 0.14)
57.58 ( 2.17) 1.0 ( 0.0) 1
| |
| 2979 :195.CA | 2988 :195.HG1 5856 :374.O4 | 0.02 4.954 ( 0.03)
33.08 ( 3.90) 1.0 ( 0.0) 1
| |
| 2986 :195.HG23| 2988 :195.HG1 5856 :374.O4 | 0.01 4.045 ( 0.08)
56.51 ( 2.93) 2.0 ( 0.0) 2
| |
| 2991 :196.N | 2988 :195.HG1 5856 :374.O4 | 0.01 4.981 ( 0.00)
59.22 ( 0.01) 1.0 ( 0.0) 1
| |
| 2982 :195.HB | 2988 :195.HG1 5851 :374.N1 | 0.01 4.863 ( 0.00)
57.05 ( 0.00) 1.0 ( 0.0) 1
| |
---------------- ---------------------------------
-------------------------------------
kindly check is it ok secondly can you please tell me know how can i
visualize results actually i want to generate graph of hydrogen bond
analysis
Regards
Sumra Wajid Abbasi
PhD Scholar
Computational Biology Lab, National Center for Bioinformatics
Quaid-e-Azam University, Islamabad-45320 Pakistan.
On Thu, Sep 19, 2013 at 7:46 PM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09 <
sumra.msbi30.iiu.edu.pk> wrote:
> Thank you for help i will definitely go for cpptraj
>
> Regards
>
> Sumra Wajid Abbasi
> PhD Scholar
> Computational Biology Lab, National Center for Bioinformatics
> Quaid-e-Azam University, Islamabad-45320 Pakistan.
>
>
> On Thu, Sep 19, 2013 at 7:42 PM, Daniel Roe <daniel.r.roe.gmail.com>wrote:
>
>> Hi,
>>
>> On Thu, Sep 19, 2013 at 8:28 AM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09
>> <sumra.msbi30.iiu.edu.pk> wrote:
>> > Hello
>> > It is also strange for me why i am receiving such warnings. As in input
>> > file i have defined only those atoms as donors/acceptors which were
>> > observed to be involved in hydrogen bond interactions at every ns using
>> VMD.
>>
>> However according to your PTRAJ output, residue 249 does not contain
>> an atom named O4:
>>
>> >> > PTRAJ: donor mask :249.O4
>> >> > Mask [:249.O4] represents 0 atoms !!!NO ATOMS DETECTED!!!
>> >> > WARNING in ptraj, donor: No atoms selected (:249.O4), ignoring...
>>
>> If you are identifying atoms by selecting them in VMD, be aware that
>> the 'residue' field numbering starts from 0. When using Amber
>> topologies in VMD it is better to use the 'resid' field, which starts
>> from 1 (this is the convention all Amber programs follow).
>>
>> You can easily test the results of mask selection in cpptraj's
>> interactive mode with the 'select' or 'parminfo' commands.
>>
>> Hope this helps,
>>
>> -Dan
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-9119 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
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>>
>
>
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Received on Fri Sep 20 2013 - 02:30:03 PDT
