On 11/23/11 4:12 PM, Hu Qiu wrote:
Hi all,
I am trying to caluculate number of hydrogen bond in my system using
the following command:
g_hbond -f model_frame2000.pdb -s md.tpr -n index_water.ndx -num
hbnum.xvg
Where the file model_frame2000.pdb is the coordinate from a frame
during my MD simulation, and the index file (index_water.ndx)contains
the index six adjacent tip5p water molecules, see following:
2559 2560 2561 2562 2563 3029 3030 3031 3032 3033 3504 3505 3506 3507
3508
5354 5355 5356 5357 5358 5394 5395 5396 5397 5398 6049 6050 6051 6052
6053
The arrangement of water oxygen is like this (rectangle), which " - "
indicates the distance is less than 0.35 nm.
OW - OW - OW
| | |
OW - OW - OW
The output hbnum.xvg gives
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
-1 4 10
As I know, the 2nd column is the number of Hydrogen bonds, and the
3ird column indicates "the Pairs within 0.35 nm, but with angle > 30".
After viewing the stucture in VMD, I found that the number of Hydrogen
bond seems to be correct. However, only 7 pairs of water oxygen
within 0.35 nm can be found (see above for the schematic drawing of
water arrangement), thus "the Pairs within 0.35 nm, but with angle >
30"should be 7-4 = 3, which is significantly lower than the value (10)
obtained in hbnum.xvg.
Third column should be simply pairs within 0.35nm, at any angle.
I don't what's wrong.
Thanks
Hu Qiu
--
Gianluca Santoni,
Institut de Biologie Structurale
41 rue Horowitz
Grenoble
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