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

David van der Spoel spoel at xray.bmc.uu.se
Wed Jul 16 15:18:16 CEST 2008 

Abil Aliev wrote:
> 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?
> 
it probably uses the position of the Cdelta. With this atom the dihedral 
angles are well-defined, but in principle it shouldn't write out a JNh.

> 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
>>>> 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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>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:        +46184714205. Fax: +4618511755.
>> spoel at xray.bmc.uu.se  spoel at gromacs.org   http://folding.bmc.uu.se
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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