Hi,
In general it's difficult to give specific advice when we can't see what
you actually tried and what kind of output you got.
On Fri, Feb 20, 2015 at 6:37 AM, Ayesha Fatima <ayeshafatima.69.gmail.com>
wrote:
> Dear Daniel and all people using Amber,
> I finally managed to get what I wanted with the hbond analysis. but
> now how do I interpret my data. In my complex, I observe that my
> ligand has an oxygen that behaves as an acceptor. This I observed from
> the general no series avgout data. in case of time series without
> specifying any acceptor or donor, I cannot see data pertaining to my
> ligand however, i specified it in the acceptor mask and now I see t
> appears in the data set.
Let me see if I understand you. First you say you ran hbond analysis
without 'series' and you see a ligand oxygen that is part of a hydrogen
bond. Next you say you ran hbond analysis with the 'series' keyword and you
don't see that hydrogen bond anymore. The only way this can happen is if
you have changed your hydrogen bond criteria (distance/angle), changed your
atom selection, or changed your trajectory. Without seeing your cpptraj
input and output from both analyses I can't say which.
> when I run the life time series, i get the
> three files with most of the frames showing zero value except in one
> or two frames, somewhere I can see the figure 2.
I'm lost here - figure 2 from what?
> In the header in the
> life.dat, I see only my ligand name and frame. what does the ligand
> residue name specify. If it specifies the residue forming the hbond,
>
You mentioned previously you got 3 files which is consistent with
performing lifetime analysis over windows - is that what you did? Otherwise
the output will look something like:
#Set Nlifetimes MaxLT AvgLT TotFrames SetName
0 19 4 1.4211 27 GLU_13.O-VAL_2.N-H
So the hydrogen bond was formed 19 total times, the max time formed was 4
frames, the average time formed was ~1.4 frames, the total time formed was
27 frames. A "lifetime" is explained briefly in the Amber 14 manual, which
I'll paste here.
’Lifetime’ in this case means ’whenever present’; data is considered
present when above or below a certain cutoff (the default is greater than
0.5, useful for hbond lifetime analysis). For example, in the case of a
hydrogen bond ’series’ dataset, if a hydrogen bond is present the set is 1,
otherwise it is 0. For example, given the dataset {0 1 1 0 1 0 0 0 1 1},
the overall average is 0.5. However, there are 3 lifetimes of lengths 2, 1,
and 2 (1 1, 1, and 1 1). The max lifetime is 2 and the average lifetime is
1.67, i.e. (2 + 1 + 2) / 3 lifetimes = 1.67.
Hope this helps,
-Dan
> which is the residue it is forming with? I looked at the AmberTools13
> information on lifetime but I am still blur on it.
> Please share your experience in this regard. I shall be grateful
> Regards
> Ayesha Fatima
>
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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 Fri Feb 20 2015 - 13:00:04 PST
