Dear Sir,
Relating to hydrogen bonding calculations, now I would like to calculate
the values for *water bridging*.
Could you kindly brief me on how to calculate the number of bridging water
from the HB calculation that I already done as indicated earlier mail in
this post?
Thanks
Vijay
On Tue, Mar 24, 2015 at 11:42 AM, Vijay Achari <glycoamber.gmail.com> wrote:
> 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 Thu Apr 16 2015 - 00:00:04 PDT
