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

[Abil Aliev]

yes, i already checked gmx_chi.c (see my previous message pasted below), and J_NHa is for proton-proton coupling between N-H and Ca-H protons. The problem is that g_chi outputs a J_NHa value for PRO, where there is no NH proton. Is this a bug?

Abil

--------------
Date: Mon, 14 Jul 2008

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
 

----------------------------------------
> Date: Tue, 15 Jul 2008 08:55:26 +0200
> From: spoel at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] definition of J-couplings in g_chi
>
> Abil Aliev wrote:
>> 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
>>
> check the source code too.
>
>> ----------------------------------------
>>> 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
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>>> Department of Biochemistry
>>> Virginia Tech
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>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
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