Hi,
On Tue, Mar 10, 2015 at 2:53 AM, Vijay Achari <glycoamber.gmail.com> wrote:
> generate two files with lifetime information. The *solute.lifetime.dat* contain
> info like:
>
> #Set Nlifetimes MaxLT AvgLT TotFrames SetName
> 0 22 1 1.0000 22 BMR_3.O16-BMR_1.O22-H22
> 1 296 346 15.6959 4646 BMR_42.O22-BMR_1.O22-H22
> 2 992 12 1.4688 1457 BMR_42.O14-BMR_1.O22-H22
> 3 1 1 1.0000 1 BMR_42.O13-BMR_1.O22-H22
> 4 189 12 1.1429 216 BMR_57.O25-BMR_1.O22-H22
> 5 462 410 12.3074 5686 BMR_57.O16-BMR_1.O22-H22
>
> I would like to know how I can go from here to calculate the hb-lifetime between
> solute and solute?
I'm not really sure I understand your question. The data output you
posted is exactly the lifetime calculation. For example, the second
set (1) contains lifetime information for the hydrogen bond between
residue 42, atom O22 and residue 1, atoms O22-H22; there were 296
individual lifetimes (i.e. the hbond formed 296 times), the max of
which lasted 346 frames, the average lifetime is ~15.7 frames. Let me
know if I'm not understanding you or if I can explain more.
-Dan
>
> I have read the pages 556-557 from AMBER 14 manual, but I find it difficult
> to see how one should start processing and getting the lifetime value.
>
> I think simple example would help me much in this case.
>
> Could you give me some example on how this can be obtained?
>
> Your help is much appreciated.
>
> Thank you.
> Vijay
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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 Tue Mar 10 2015 - 07:30:04 PDT
