[gmx-users] definition of J-couplings in g_chi
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jul 30 09:36:38 CEST 2008
Abil Aliev wrote:
> Fair enough! How did you calculate your averaged J couplings in g_chi? We just did a quick test for the { "J_HaC'", 4.0, 1.1, 0.1, 0.0, 0.0, 0.0 } set and got somewhat different results (1.42 Hz vs 0.98 Hz by g_chi). In our calculations we calculate the J-coupling value in each frame using the dihedral angle value from g_angle, then the sum of all the J-couplings is divided by the total number of frames to find the averaged J value.
>
The same way as you describe. In other words either g_chi or your
analysis is wrong (or both :)). Please double check the source code.
> Abil
>
>
> ----------------------------------------
>> Date: Wed, 16 Jul 2008 15:18:16 +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:
>>> 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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>
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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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