[gmx-users] definition of J-couplings in g_chi
Abil Aliev
armi510 at live.co.uk
Tue Jul 29 19:02:58 CEST 2008
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.
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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>>>>> --
>>>>> ========================================
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>>>>> Justin A. Lemkul
>>>>> Graduate Research Assistant
>>>>> Department of Biochemistry
>>>>> Virginia Tech
>>>>> Blacksburg, VA
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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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