Dear Daniel,
If you dont mind, could you provide the citation relevent for the
implementation of HB lifetime calcultion?
Thanks in advance.
Vijay
On Sun, Mar 22, 2015 at 1:23 PM, Vijay Achari <glycoamber.gmail.com> wrote:
> Dear Daniel,
>
> I was away and now I am back.
>
> Thanks for your reply.
>
> Since I am working on disaccharide glycolipids, I have 11 acceptors
> (O11,O12,O13,O14,O15,O16,O22,O23,O24,O25,O26), and 7 hydroxyl groups
> (O12-H12, O13-H13, O16-H16, O22-H22, O23-H23, O24-H24, O26-H26).
>
> My main target was to know, in average, how long each acceptor (O) of a
> glycolipid involve in hydrogen bonding interaction no matter which donor is
> involved, in the glycolipid bilayer assembly.
>
> So to achieve this, I selected columns only with "O22" (for example:
> BMR_42.O22-BMR, BMR_49.O22-BMR, BMR_59.O22-BMR, BMR_23.O22-BMR,
> BMR_10.O22-BMR BMR_61.O22-BMR) and sum up all the "1s" and divided with
> the total number of frames involved. I repeated this procedure for each
> acceptors.
>
> If I am not mistaken, I guess what you have suggested is what I want
> actually. But I did not use *readdata* and *lifeltime* commands to get
> the final value. I used an awk script to do the selections column wise and
> average over all frames.
>
> Welcome any feedback from your side to enhance my understanding.
>
> Thank you.
> Vijay
>
>
>
>
> On Sun, Mar 22, 2015 at 12:06 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
>> Hi,
>>
>> You still haven't said whether I was right or wrong about you wanting
>> to calculate the lifetime of a certain solute atom (or residue) being
>> involved in *any* hydrogen bond. Since you haven't said no, I will
>> proceed on the assumption that this is what you want. In that case
>> this is the procedure I would use.
>>
>> 1) Calculate the hydrogen bond time series data (you have done this).
>>
>> 2) Use a script to sum up all columns involving your atom/residue of
>> interest. This could be as simple as visually identifying which
>> columns contain the data you need (e.g. columns 2, 4, 5, and 7) and
>> using something like awk:
>>
>> awk '{print $2 + $4 + $5 + $7}' solutehb.dat > sum.dat
>>
>> 3) Read the summed data back into cpptraj with readdata:
>>
>> readdata sum.dat
>>
>> 4) Perform lifetime analysis on the summed data. The default settings
>> for cutoff etc will still work since anything greater than 0 means a
>> hydrogen bond is present:
>>
>> lifetime sum.dat out life.sum.dat ...
>>
>> -Dan
>>
>> On Mon, Mar 16, 2015 at 10:50 AM, Vijay Achari <glycoamber.gmail.com>
>> wrote:
>> > Dear Dan,
>> >
>> > Below is the example you gave to explain on how the calculation of HB
>> can
>> > done with raw data.
>> >
>> >
>> > HB1-1 HB1-2
>> > 1 0
>> > 0 1
>> > 1 0
>> > 1 1
>> >
>> > Using the method I illustrated before you'd come up with an average of
>> > (5 / 4 = 1.25). However, the actual answer of how often is HB1
>> > involved in a hydrogen bond is clearly all 4 frames, since when HB1-1
>> > is broken, HB1-2 is formed, so its always involved in some kind of
>> > hydrogen bond. So to do what you want you will need to write out the
>> > raw time series data, sum up the columns corresponding to the hydrogen
>> > bonds you are interested in, then run 'lifetime' analysis on that data
>> > set. So using the above sets as an example, the set I would actually
>> > run lifetime analysis on would look like:
>> >
>> >
>> > Relating to the above example, I understand that we need to add the "1"s
>> > and divide by total number of lines.
>> >
>> > (total of all "1"s) / (total rows with "1"s)
>> >
>> >
>> > So how with the example below? (I modified the above sample).
>> >
>> > HB1-1 HB1-2
>> > 1 0
>> > 0 1
>> > 1 0
>> > 1 1
>> > 0 1
>> > 0 0
>> > 0 0
>> >
>> > For the above example is the the average is 6/7 or 6/5. The number 7
>> > stand for total number of rows and the later stand for rows with the
>> > presence of "1" (at least once).
>> >
>> > Means do I need to count the total rows or the rows with the occurrence
>> of
>> > "1" only?
>> >
>> >
>> >
>> > Your explanation would help me to write the script.
>> >
>> > Thanks.
>> >
>> >
>> >
>> > On Thu, Mar 12, 2015 at 4:53 PM, Vijay Achari <glycoamber.gmail.com>
>> wrote:
>> >
>> >> Dear Dan,
>> >>
>> >> Following your explanation, I would like to verify few things.
>> >>
>> >> #1) The file that contains the raw data; is this one "solutehb.dat"
>> >>
>> >> if yes,
>> >>
>> >> #2) The format of the data in the file is as below?
>> >>
>> >> #Frame *BMR_42.O22-BMR_1.O23-H23* BMR_49.O13-BMR_1.O13-H13
>> >> BMR_59.O13-BMR_2.O22-H22 BMR_10.O13-BMR_2.O26-H26 BMR_61.O26-BMR_3
>> .O22-H22
>> >> BMR_23.
>> >> O25-BMR_4.O12-H12 BMR_23.O26-BMR_4.O13-H13 BMR_23.O25-BMR_4.O13-H13
>> >> BMR_20.O13-BMR_5.O22-H22 BMR_10.O24-BMR_6.O13-H13 BMR_41.O23-BMR_7
>> .O23-H2
>> >> 3 BMR_41.O24-BMR_7.O23-H23 ....
>> >>
>> >>
>> >> * 1 * 1
>> >> 1 1 1
>> >> 1 1 1
>> >> 1 1 1
>> >> 1 1 1
>> >> 1 1 1
>> >> 1 1 1
>> >> 1 1
>> >> 1 1
>> >> 1 1
>> >> 1 1
>> >> 1 1
>> >> 1 1
>> >> 1 1
>> >> 1 1
>> >> 1 1
>> >> 1 1
>> >> 1 1
>> >> 1 1
>> >> 1 1 1 . . .
>> >>
>> >>
>> >> #3) So need I operate on this file?
>> >>
>> >> #4) Is the first data "BMR_42.O22-BMR_1.O23-H23" is corresponding to
>> the
>> >> value "1" (below #2)
>> >>
>> >> Thank you.
>> >>
>> >>
>> >>
>> >>
>> >> On Wed, Mar 11, 2015 at 11:11 PM, Daniel Roe <daniel.r.roe.gmail.com>
>> >> wrote:
>> >>
>> >>> Hi,
>> >>>
>> >>> Sorry, it's not clear to me what you're trying to calculate. You said
>> >>> "I want to know the lifetime of HB for O22 (ACCEPTOR) atom only"; do
>> >>> you want the average lifetime of any given O22 involved in a hydrogen
>> >>> bond? In that case you will probably need to write your own script for
>> >>> it for the time being. I'll try to illustrate why with an example. Say
>> >>> I want to ask how often is BMR_49.O22 involved in any hydrogen bond
>> as
>> >>> an acceptor. I could naively sum up the total number of frames the
>> >>> bond is present (TotFrames) for each instance of this acceptor atom
>> >>> and then divide by the total number of lifetimes:
>> >>>
>> >>> 4 20 5 1.8500 37
>> >>> BMR_49.O22-BMR_1.O26-H26
>> >>> 7 28 2 1.0357 29
>> >>> BMR_49.O22-BMR_1.O13-H13
>> >>>
>> >>> the total number frames there is a hydrogen bond is 66, and the total
>> >>> number of lifetimes is 48, so the average lifetime for BMR_49.O22
>> >>> involved in any hydrogen bond (given the data here) is 1.375 frames.
>> >>> However, this is only true if the data were sequential, because it
>> >>> doesn't take into account the times when one is present and the other
>> >>> isn't. For example, given this hydrogen bond data (where HB1
>> >>> represents a single acceptor):
>> >>>
>> >>> HB1-1 HB1-2
>> >>> 1 0
>> >>> 0 1
>> >>> 1 0
>> >>> 1 1
>> >>>
>> >>> Using the method I illustrated before you'd come up with an average of
>> >>> (5 / 4 = 1.25). However, the actual answer of how often is HB1
>> >>> involved in a hydrogen bond is clearly all 4 frames, since when HB1-1
>> >>> is broken, HB1-2 is formed, so its always involved in some kind of
>> >>> hydrogen bond. So to do what you want you will need to write out the
>> >>> raw time series data, sum up the columns corresponding to the hydrogen
>> >>> bonds you are interested in, then run 'lifetime' analysis on that data
>> >>> set. So using the above sets as an example, the set I would actually
>> >>> run lifetime analysis on would look like:
>> >>>
>> >>> (HB1-1)+(HB1-2)
>> >>> 1
>> >>> 1
>> >>> 1
>> >>> 2
>> >>>
>> >>> Hope this helps,
>> >>>
>> >>> -Dan
>> >>>
>> >>> On Wed, Mar 11, 2015 at 12:57 AM, Vijay Achari <glycoamber.gmail.com>
>> >>> wrote:
>> >>> > Dear Dan,
>> >>> >
>> >>> > In my case the time gap in between two frames (taken for analysis)
>> is
>> >>> 5ps.
>> >>> >
>> >>> > #Set Nlifetimes MaxLT AvgLT TotFrames SetName
>> >>> > 0 17 215 55.7059 947
>> >>> > BMR_42.O22-BMR_1.O23-H23
>> >>> > 1 1 1 1.0000 1
>> >>> > BMR_42.O23-BMR_1.O23-H23
>> >>> > 2 31 3 1.0968 34
>> >>> > BMR_31.O22-BMR_1.O26-H26
>> >>> > 3 11 2 1.0909 12
>> >>> > BMR_31.O13-BMR_1.O26-H26
>> >>> > 4 20 5 1.8500 37
>> >>> > BMR_49.O22-BMR_1.O26-H26
>> >>> > 5 24 4 1.7917 43
>> >>> > BMR_49.O23-BMR_1.O26-H26
>> >>> > 6 41 2 1.0488 43
>> >>> > BMR_49.O12-BMR_1.O12-H12
>> >>> > 7 28 2 1.0357 29
>> >>> > BMR_49.O22-BMR_1.O13-H13
>> >>> > 8 1 1000 1000.0000 1000
>> >>> > BMR_49.O13-BMR_1.O13-H13
>> >>> > 9 1 1 1.0000 1
>> >>> > BMR_22.O12-BMR_2.O22-H22
>> >>> > 10 50 62 18.9400 947
>> >>> > BMR_59.O13-BMR_2.O22-H22
>> >>> > 11 1 1 1.0000 1
>> >>> > BMR_59.O25-BMR_2.O23-H23
>> >>> > 12 34 5 1.1471 39
>> >>> > BMR_59.O13-BMR_2.O23-H23
>> >>> > 13 7 6 2.1429 15
>> >>> > BMR_59.O26-BMR_2.O24-H24
>> >>> > 14 6 8 3.6667 22
>> >>> > BMR_59.O25-BMR_2.O24-H24
>> >>> > 15 28 2 1.1071 31
>> >>> > BMR_10.O26-BMR_2.O26-H26
>> >>> > 16 52 121 15.1346 787
>> >>> > BMR_10.O25-BMR_2.O26-H26
>> >>> > 17 65 9 1.9231 125
>> >>> > BMR_10.O13-BMR_2.O26-H26
>> >>> > 18 4 4 2.2500 9
>> >>> > BMR_59.O26-BMR_2.O26-H26
>> >>> > 19 9 1 1.0000 9
>> >>> > BMR_22.O15-BMR_2.O13-H13
>> >>> > 20 1 1 1.0000 1
>> >>> > BMR_10.O11-BMR_2.O16-H16
>> >>> > 21 7 2 1.1429 8
>> >>> > BMR_53.O13-BMR_2.O16-H16
>> >>> > 22 2 3 2.5000 5
>> >>> > BMR_33.O13-BMR_3.O22-H22
>> >>> > 23 97 54 6.8247 662
>> >>> > BMR_61.O26-BMR_3.O22-H22
>> >>> > 24 1 1 1.0000 1
>> >>> > BMR_29.O26-BMR_3.O23-H23
>> >>> > 25 31 36 3.3226 103
>> >>> > BMR_29.O16-BMR_3.O23-H23
>> >>> > 26 22 2 1.2273 27
>> >>> > BMR_30.O22-BMR_3.O23-H23
>> >>> > 27 4 1 1.0000 4
>> >>> > BMR_33.O22-BMR_3.O23-H23
>> >>> > 28 38 2 1.1316 43
>> >>> > BMR_33.O13-BMR_3.O23-H23
>> >>> > (there are more than 2000 lines, but I work on only 28 lines to get
>> some
>> >>> > understanding)
>> >>> >
>> >>> >
>> >>> > For clarity, I shall show you how I worked on the given results
>> above.
>> >>> >
>> >>> > I want to know the lifetime of HB for O22 (ACCEPTOR) atom only. So,
>> I
>> >>> did
>> >>> > in this way,
>> >>> >
>> >>> > 1) sum the values from column AvgLT for the only occurrences of O22.
>> >>> > 2) than find the average of that, where the denominator would be the
>> >>> number
>> >>> > of occurrences of O22.
>> >>> >
>> >>> > Based on the above steps, the results are :
>> >>> >
>> >>> > O22 occur 6 times,
>> >>> > sum of O22 is 61.916, and
>> >>> > average of O22 is 10.319.
>> >>> >
>> >>> > So, I figured out the lifetime of O22 would be 10.319 x 5ps =
>> 51.595
>> >>> ps.
>> >>> >
>> >>> > Is this correct? Did I choose the correct column "AvgLT"?
>> >>> >
>> >>> > I hope to get some feedback if this is correct way to do it.
>> >>> >
>> >>> > Many thanks in advance.
>> >>> >
>> >>> > Vijay
>> >>> >
>> >>> >
>> >>> > On Wed, Mar 11, 2015 at 11:50 AM, Daniel Roe <
>> daniel.r.roe.gmail.com>
>> >>> wrote:
>> >>> >
>> >>> >> On Tue, Mar 10, 2015 at 9:24 PM, Vijay Achari <
>> glycoamber.gmail.com>
>> >>> >> wrote:
>> >>> >> > Could you explain on how to get the lifetime value in pico second
>> >>> (ps)?
>> >>> >>
>> >>> >> This depends on how often you recorded your coordinate trajectory.
>> For
>> >>> >> example, say you ran a simulation with a timestep of 2 fs (dt=0.002
>> >>> >> ps) and you recorded a trajectory frame every 500 steps (ntwx=500).
>> >>> >> This means that each frame in your trajectory has been recorded at
>> 1
>> >>> >> ps intervals. However, say you recorded your trajectory every 5000
>> >>> >> steps instead - your trajectory then will have been recorded at 10
>> ps
>> >>> >> intervals. Since lifetimes are always given in frames, it should be
>> >>> >> easy to convert to ps based on how often your coordinate trajectory
>> >>> >> was written to (e.g. in the latter case a max lifetime of 1 frame
>> >>> >> would mean 10 ps).
>> >>> >>
>> >>> >> Hope this helps,
>> >>> >>
>> >>> >> -Dan
>> >>> >>
>> >>> >> >
>> >>> >> > Thanks in advance.
>> >>> >> > Vijay
>> >>> >> >
>> >>> >> >
>> >>> >> > On Tue, Mar 10, 2015 at 10:15 PM, Daniel Roe <
>> daniel.r.roe.gmail.com
>> >>> >
>> >>> >> wrote:
>> >>> >> >
>> >>> >> >> 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
>> >>> >> >> > _______________________________________________
>> >>> >> >> > AMBER mailing list
>> >>> >> >> > AMBER.ambermd.org
>> >>> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >>> >> >>
>> >>> >> >>
>> >>> >> >>
>> >>> >> >> --
>> >>> >> >> -------------------------
>> >>> >> >> 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)
>> >>> >> >>
>> >>> >> >> _______________________________________________
>> >>> >> >> AMBER mailing list
>> >>> >> >> AMBER.ambermd.org
>> >>> >> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>> >> >>
>> >>> >> > _______________________________________________
>> >>> >> > AMBER mailing list
>> >>> >> > AMBER.ambermd.org
>> >>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >>> >>
>> >>> >>
>> >>> >>
>> >>> >> --
>> >>> >> -------------------------
>> >>> >> 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)
>> >>> >>
>> >>> >> _______________________________________________
>> >>> >> AMBER mailing list
>> >>> >> AMBER.ambermd.org
>> >>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>> >>
>> >>> > _______________________________________________
>> >>> > AMBER mailing list
>> >>> > AMBER.ambermd.org
>> >>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> -------------------------
>> >>> 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)
>> >>>
>> >>> _______________________________________________
>> >>> AMBER mailing list
>> >>> AMBER.ambermd.org
>> >>> http://lists.ambermd.org/mailman/listinfo/amber
>> >>>
>> >>
>> >>
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> 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)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Mon Mar 23 2015 - 21:00:02 PDT
