Re: [AMBER] Evaluating hydrogen boding lifetime

From: Vijay Achari <glycoamber.gmail.com>
Date: Wed, 11 Mar 2015 11:24:34 +0800

Dear Daniel,

Thanks for the brief explanation.

An excerpt from AMBER14 manual - page 557 says :

"

*For example, given the dataset {0 1 1 0 1 0 0 0 1 1}, theoverall 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 2and the average lifetime is 1.67, i.e. (2 + 1 +
2) / 3 lifetimes = 1.67*."

>From the above lines I think I understand the *Nlifetimes, MaxLT, AvgLT,
TotFrames, SetName*.

By the way, what I am looking for is the lifetime value in pico seconds
(ps).

For example a paper (*Phys. Chem. Chem. Phys.*, 2014, *16.* 324-334)
reports the HB lifetime in ps (Table 3).

Could you explain on how to get the lifetime value in pico second (ps)?

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:
> 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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> > 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)
>
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>
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Received on Tue Mar 10 2015 - 20:30:03 PDT
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