Dear amber user
I am simulating water and disccharide solution having 25 disccharide and
1000 water. I want to calculate hbond around solute. this my pitraj input..
trajin NVT-production1.mdcrd
trajin NVT-production2.mdcrd
trajin NVT-production3.mdcrd
donor mask :1-50.O2
acceptor WAT O H1
acceptor WAT O H2
hbond distance 3.5 angle 120.0 nosort series time out hb.dat
and the result is...
HBOND SUMMARY:
Data was saved to series time, output to file hb.dat,
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
| 1086 :49.O2 | 2349 :458.H2 2347 :458.O | 0.11 2.791 ( 0.00)
24.78 ( 0.00) 1.0 ( 0.0) 1
|. |
| 1086 :49.O2 | 2348 :458.H1 2347 :458.O | 0.11 3.431 ( 0.00)
58.37 ( 0.00) 1.0 ( 0.0) 1
|. |
| 1063 :48.O2 | 4553 :1193.H1 4552 :1193.O | 0.11 2.941 ( 0.00)
49.95 ( 0.00) 1.0 ( 0.0) 1 |
. |
| 1063 :48.O2 | 2199 :408.H2 2197 :408.O | 0.57 2.793 ( 0.10)
25.49 (13.99) 5.0 ( 0.0) 5 |
.. |
| 1041 :47.O2 | 4886 :1304.H1 4885 :1304.O | 0.11 3.330 ( 0.00)
37.16 ( 0.00) 1.0 ( 0.0) 1 |
. |
| 1041 :47.O2 | 3749 :925.H1 3748 :925.O | 0.23 2.817 ( 0.06)
18.98 ( 1.14) 1.0 ( 0.0) 1
|. |
| 1041 :47.O2 | 2730 :585.H2 2728 :585.O | 0.46 3.051 ( 0.23)
20.32 (20.93) 4.0 ( 0.0) 4
| .. |
| 1041 :47.O2 | 2445 :490.H2 2443 :490.O | 0.23 2.931 ( 0.12)
12.61 ( 0.29) 1.0 ( 0.0) 1 |
.. |
| 1041 :47.O2 | 2444 :490.H1 2443 :490.O | 0.11 2.629 ( 0.00)
16.68 ( 0.00) 1.0 ( 0.0) 1 |
. |
| 1041 :47.O2 | 1365 :130.H2 1363 :130.O | 0.34 3.147 ( 0.34)
36.27 (18.18) 1.5 ( 0.5) 2
| . |
| 1041 :47.O2 | 1364 :130.H1 1363 :130.O | 0.68 2.798 ( 0.15)
23.93 ( 9.49) 6.0 ( 0.0) 6
| - |
| 1018 :46.O2 | 4784 :1270.H1 4783 :1270.O | 0.11 3.373 ( 0.00)
58.62 ( 0.00) 1.0 ( 0.0) 1 |
. |
| 1018 :46.O2 | 4769 :1265.H1 4768 :1265.O | 0.57 2.862 ( 0.16)
28.43 (12.59) 1.7 ( 0.5) 2 | ..
. |
| 1018 :46.O2 | 3468 :831.H2 3466 :831.O | 0.23 3.256 ( 0.23)
33.04 (17.93) 1.0 ( 0.0) 1 |
. |
| 973 :44.O2 | 4770 :1265.H2 4768 :1265.O | 0.46 3.054 ( 0.21)
34.25 (14.79) 2.0 ( 0.0) 2 |
.. |
| 973 :44.O2 | 4769 :1265.H1 4768 :1265.O | 1.26 2.903 ( 0.19)
25.56 (11.61) 2.8 ( 2.5) 7 |
..-. |
| 973 :44.O2 | 3354 :793.H2 3352 :793.O | 0.11 2.803 ( 0.00)
4.16 ( 0.00) 1.0 ( 0.0) 1 |
. |
| 973 :44.O2 | 3227 :751.H1 3226 :751.O | 0.11 2.783 ( 0.00)
19.23 ( 0.00) 1.0 ( 0.0) 1 |
. |
| 973 :44.O2 | 2718 :581.H2 2716 :581.O | 0.57 2.856 ( 0.26)
20.05 (13.26) 2.5 ( 1.5) 4 | .
- |
| 973 :44.O2 | 2717 :581.H1 2716 :581.O | 0.68 2.853 ( 0.13)
25.13 ( 7.35) 6.0 ( 0.0) 6 |
- |
| 973 :44.O2 | 2
actualy i want to calculate hbond vs time or hydrogenbond per solute.How i
extract this from the above data?? i am some difficulty any help will
greatfuly thank.
thanking you
subrata
IITGuwahati
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Received on Fri Jul 22 2011 - 03:30:02 PDT
