Re: [AMBER] H-bond analysis interpratation

From: Sangita Kachhap <sangita.imtech.res.in>
Date: Thu, 6 Jan 2011 10:17:14 +0530 (IST)

 Thank you Thomas Cheatham, now I got my answer.

>
>> Here I want to know one more thing what is the default value of time, Is it 1
>> ?
>
> The default value is 1.0 * [the spacing between frames]. If the spacing
> between frames is 5 ns, then you will only get data every 5 ns. If you
> dump every ps, then the time is 1 ps.
>
>>
>> In Amber tutorial:- http://ambermd.org/tutorials/basic/tutorial3/section6.htm
>>
>> Occupancy of H-bonding (last column)is define in form of time of MD run i.e.
>> percentage occupency is written after every 5ns of trajectory.
>>
>> Is it possible in amber11 to get such form of result ?
>
> AmberTools prints out a larger number of "points" (50) for this pseudo
> h-bond time course plot...
>
>
> | 292 :10.O5' | 287 :9.HO'2 286 :9.O2' | 24.30 3.079 ( 0.22)
> 39.59 (12.43) 2.4 ( 6.6) 109
> |---.--.-....-o.@@o.....--.-......-....--.--.--...-|
>
> Therefore the spacing in this plot is effectively the (total number of
> frames read in) / 50. To alter this behavior would require code changes.
>
> --tec3
>
>
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>


Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH


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Received on Wed Jan 05 2011 - 21:00:03 PST
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