Yes - 104 continuous frames where a hydrogen bond is present (based on
the specified geometric criteria) would be a single lifetime of length
104.
-Dan
On Mon, Mar 14, 2016 at 2:37 PM, Krantzman, Kristin D
<KrantzmanK.cofc.edu> wrote:
> Oops, I meant ~ 104 continuous frames.
> ________________________________________
> From: Krantzman, Kristin D [KrantzmanK.cofc.edu]
> Sent: Monday, March 14, 2016 4:34 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Lifetime analysis of backbone hydrogen bonds
>
> Dear Daniel,
> This was very helpful!
> Therefore, if one residue has 104 frames, this means that the hydrogen bond was present for ~ 104 frames. Just making sure that I understand.
> Thanks, Kristin
> ________________________________________
> From: Daniel Roe [daniel.r.roe.gmail.com]
> Sent: Monday, March 14, 2016 3:45 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Lifetime analysis of backbone hydrogen bonds
>
> On Mon, Mar 14, 2016 at 1:28 PM, Krantzman, Kristin D
> <KrantzmanK.cofc.edu> wrote:
>> I am not sure what the items are in Nlifetime, MaxLT, AvgLT and TotFrames. I
>
> Nlifetime is the total number of lifetimes (i.e. contiguous segments
> of time where the hbond was "present") experienced by that hbond.
> MaxLT is the maximum lifetime observed in frames.
> AvgLT is the average over all lifetimes in frames.
> TotFrames is the total number of frames over all lifetimes.
>
>> The second file called crv.backbone.lifetime.dat
>> has 26 frames with 60 curves.
>> I have read the information in the Amber15 manual, but I am still not understanding exactly what the information means.
>
> A "lifetime curve" is essentially the curve created by adding all
> observed lifetimes on top of each other (and normalized so that 0.0 is
> 1.0 by default). For example, take the raw data set (this could be any
> individual *[solutehb] series data):
>
> 01111000110000010011110
>
> Each contiguous segment of '1' (i.e. "present") is a lifetime, so for
> this set of data 4 lifetimes are observed, with lengths of 4, 2, 1,
> and 4. Taken individually they look like:
>
> 1111
> 11
> 1
> 1111
>
> The raw "lifetime curve" is then calculated as follows: for each frame
> in all lifetimes up to the max lifetime (in this case 4) sum up the
> individual lifetimes. So in this case the raw lifetime curve would
> look like:
>
> 4 3 2 2
>
> You can read this as all four lifetimes are present at frame 1, only
> three lifetimes are still present at frame 2, and only two lifetimes
> are still present at frames 3 and 4. This gives you information about
> the dynamic behavior of the lifetime (is it long-lived, does it decay
> quickly, etc).
>
> Hope this helps,
>
> -Dan
>
>> If you have any guidance or suggest a reference that I could read, I would appreciate it.
>> Thanks in advance!
>> Best, Kristin D. Krantzman
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>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> https://urldefense.proofpoint.com/v2/url?u=http-3A__home.chpc.utah.edu_-7Echeatham_&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=wuSDjSHAtEcpjt79xVDv7jOiD6JtkwBZT6yxg3PRNRE&s=7nKkgKvYlPByGATtlcUvMi-58XyfR6b7Dz16EuUf_Zg&e=
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Mar 14 2016 - 14:00:05 PDT
