Hello
I have been performing hydrogen bonding calculations using the ptraj script
using Amber and I had got an output showing the hydrogen bonding
pattern. The result, I understand shows the donor, acceptorH, acceptor atoms
followed by the % occupancy, distance, angle, lifetime and the maxocc. But I
am not sure what the numbers in the paranthesis represent. In the case of
distance and angle, I presume it gives the standard deviation, but what do
the ones in the paranthesis for lifetime mean? I searched the archive for
possible explanation and the tutorial but could not get it properly. It
would be really helpful if someone could direct me on this issue
DONOR ACCEPTORH ACCEPTOR
atom# :res.atom atom# :res.atom atom# :res.atom % occupied distance
angle lifetime maxocc
| 4237 :266.O1P | 2003 :129.HH22 2001 :129.NH2 | 96.89 2.775
( 0.09) 24.46 (10.36) 33.4 ( 43.0) 294
|...............*...*|
| 8727 :539.O1P | 6490 :402.HH12 6488 :402.NH1 | 90.53 2.793
( 0.09) 25.59 ( 9.29) 11.7 ( 15.8) 96 |*x**x.
.*.**.******.*|
| 4257 :266.N1 | 8845 :542.H3 8844 :542.N3 | 68.96
2.900 ( 0.06) 15.21 ( 8.61) 3.5 ( 3.4) 27
|xxxxxxxxoxoooxxxx**x|
| 8747 :539.N1 | 4355 :269.H3 4354 :269.N3 | 64.01
2.903 ( 0.06) 16.84 ( 9.18) 3.0 ( 2.8) 22
|xxxxxxooxxxoxxxxxoox|
Thanks and regards,
Srivatsan
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Received on Fri Apr 23 2010 - 03:00:03 PDT
