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: [EMAIL PROTECTED]
> To: gmx-users@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: [EMAIL PROTECTED]
>> To: gmx-users@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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