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