[gmx-users] definition of J-couplings in g_chi

[Abil Aliev]

There is a clue in the gmx_c.file, which says:

  { "J_NHa",     6.51, -1.76,  1.6, -M_PI/3,   0.0,  0.0 }

The above A,B,C values are the same as in the Bax paper in JACS, 1993 115 7772 and are for homonuclear 3J(NH,CHa) couplings

    { "J_HaC'",    4.0,   1.1,   0.1,  0.0,      0.0,  0.0 }, 
The same set of coefficients as in JACS 1995 117 1810 for the Karplus equation for a heteronuclear 3J(1H,13C) coupling between the NH proton and the C' carbon (why use J_HaC' if it is J_NHC' ??)

    { "J_HaN",   -0.88, -0.61,-0.27,M_PI/3,  0.0,  0.0 }

The same as in JACS 1995 117 1810 for the Karplus equation for a heteronuclear 3J(1H,15N) coupling between the Ha proton and the 15N nucleus which is 3 bonds away from Ha.

Going back to the reason for my question, when running g_chi for a PRO containing peptide there should be no output for PRO in the J_NHa column in chi.log as there is no proton attached to N of PRO. But g_chi insists that there is J_NHa coupling for PRO ?!

Abil

----------------------------------------
> From: armi510 at live.co.uk
> To: gmx-users at gromacs.org
> Subject: RE: [gmx-users] definition of J-couplings in g_chi
> Date: Mon, 14 Jul 2008 11:27:33 +0000
> 
> 
> Justin, thanks for your response. I am merely trying to understand whether J_NHa refers to 15N,1H or N1H_Ca1H coupling. The same goes to other J namings used
>  
> ----------------------------------------
>> Date: Mon, 14 Jul 2008 07:20:53 -0400
>> From: jalemkul at vt.edu
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] definition of J-couplings in g_chi
>> 
>> The manual will not spell everything out for you, but a little bit of background 
>> reading will give you the answer.  From g_chi -h:
>> 
>> "...
>> (b) The NMR 3J coupling constants from the Karplus equation.
>> ..."
>> 
>> The curious individual would then probably look up what the Karplus equation is, 
>> and via Google search, arrive here:
>> 
>> http://en.wikipedia.org/wiki/Karplus_equation
>> 
>> The answers are out there, and if you don't know what a term or parameter means, 
>> Google is usually your friend.
>> 
>> -Justin
>> 
>> Abil Aliev wrote:
>>> Hello,
>>> 
>>> I couldnt find definitions of vicinal J-couplings used in g_chi from the online manual. These are the J-couplings listed by g_chi:
>>> 
>>> J_NHa   J_HaC'   J_NHCb   J_Ci-1Hai    J_HaN   JHaHb2   JHaHb3
>>> 
>>> Thank you,
>>> Abil
>>> 
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>> 
>> -- 
>> ========================================
>> 
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> 
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