Thanks for your kind reply sir.
Best regards
Vijay
On Fri, Apr 17, 2015 at 10:12 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Thu, Apr 16, 2015 at 11:47 PM, Vijay Achari <glycoamber.gmail.com>
> wrote:
> >
> > Questeion: I am not sure how to go about to find the number of bridging
> > from this info. Appreciate if I get some hint from here.
>
> The total number of bridging waters is in 'nhb.dat'. If you mean you
> need the total number of bridging waters per unique bridge this
> information is not stored.
>
> > #Q(2)
> > This question is related to the HB lifetime calculation. I came to know
> > that the HB lifetimes can be calculated based on 4 types of definitions.
> i)
> > continues lifetime, ii) intermittent lifetime, iii) kinetic lifetime, and
> > iv) SSP (stable state picture model) - reference [ Acta Phys. -Chim. Sin.
> > 2011, 27 (11), 2547-2552 ]. Since I am writing a paper now, I need the
> > citation of on which the AMBER is used to calculate the hydrogen bonding
> > lifetimes. I have scanned through the AMBER manual (by typing word
> > "lifetime"), but could not find any related citation. Appreciate if you
> > could point one.
>
> CPPTRAJ has it's own definition of "lifetime" (which was originally
> implemented in PTRAJ's 'hbond' command) which is described in the
> manual (Amber 14 section 28.12.11), so just cite the PTRAJ/CPPTRAJ
> paper:
>
> Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ:
> Software for Processing and Analysis of Molecular Dynamics Trajectory
> Data". J. Chem. Theory Comput., 2013, 9 (7), pp 3084-3095.
>
> -Dan
>
> >
> > Many thanks in advance.
> > Regards
> > Vijay
> >
> >
> >
> >
> > On Thu, Apr 16, 2015 at 10:41 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> Hi,
> >>
> >> On Thu, Apr 16, 2015 at 12:41 AM, Vijay Achari <glycoamber.gmail.com>
> >> wrote:
> >> > 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?
> >>
> >> If you specified 'solventdonor' or 'solventacceptor' then the bridging
> >> calculation is performed. It is written the file specified by
> >> bridgeout, or solvout, or avgout (in order of precedence). If none of
> >> that is specified it is written to STDOUT. See the manual for more
> >> details.
> >>
> >> -Dan
> >>
> >> >
> >> > 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
> >> >>>>
> >> >>>
> >> >>>
> >> >>
> >> > _______________________________________________
> >> > 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 Fri Apr 17 2015 - 21:00:02 PDT
