Re: [AMBER] Calculation of Intramolecular hydrogen bonding using ptraj

From: Thomas Cheatham III <tec3.utah.edu>
Date: Tue, 27 Jul 2010 11:15:43 -0600 (Mountain Daylight Time)

> Can you please explain me regarding how I can interpret my result from as
> shown below (first two line of the output are only shown).

Hmmn, seems I need to update the manual.

> What does the number in the parenthesis beside the distance,angle values
> mean. Is it the deviation?
> What does lifetime and maxoccupancy give me?
>
> atom# :res.atom atom# :res.atom atom# :res.atom %occupied
> distance angle lifetime maxocc
> | 115 :1.O10 | 104 :1.H20 92 :1.O8 | 96.06 2.818 ( 0.21)
> 34.14 (28.58) 45.5 ( 72.3) 390 |.@@@x@
> .*@@*@@@@@@@@@@@*.x*@@@**@**@@@@@@@@@*@@@@@|

The h-bond is formed for 96% of the simulation; average distance of 2.818
A with a 0.21 stddev. The lifetime is 45.5 frames (i.e. if you assume 1
ps between frames, the average lifetime of the h-bond is 45.5 ps; note
that this value will depend on the distance cutofff). Finally the maxocc
represents the longest time an h-bond was formed was 390 frames. You can
likely see this as fluctuations in the distance > the h-bond cutoff
specified. --tec3

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Received on Tue Jul 27 2010 - 10:30:05 PDT
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