This is part of the isdb module

Calculates 3J coupling constants for a dihedral angle.

The J-coupling between two atoms is given by the Karplus relation:

\[ ^3J(\theta)=A\cos^2(\theta+\Delta\theta)+B\cos(\theta+\Delta\theta)+C \]

where \(A\), \(B\) and \(C\) are the Karplus parameters and \(\Delta\theta\) is an additional constant added on to the dihedral angle \(\theta\). The Karplus parameters are determined empirically and are dependent on the type of J-coupling.

This collective variable computes the J-couplings for a set of atoms defining a dihedral angle. You can specify the atoms involved using the MOLINFO notation. You can also specify the experimental couplings using the COUPLING keywords. These will be included in the output. You must choose the type of coupling using the type keyword, you can also supply custom Karplus parameters using TYPE=CUSTOM and the A, B, C and SHIFT keywords. You will need to make sure you are using the correct dihedral angle:

Ha-N: \(\psi\)
Ha-HN: \(\phi\)
N-C \(\gamma\): \(\chi_1\)
CO-C \(\gamma\): \(\chi_1\)

J-couplings can be used to calculate a Metainference score using the internal keyword DOSCORE and all the options of METAINFERENCE .

Examples

In the following example we calculate the Ha-N J-coupling from a set of atoms involved in dihedral \(\psi\) angles in the peptide backbone. We also add the experimental data points and compute the correlation and other measures and finally print the results.

Click on the labels of the actions for more information on what each action computes

#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO MOLTYPEcompulsory keyword ( default=protein )
what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA
are compatible 
=protein STRUCTUREcompulsory keyword 
a file in pdb format containing a reference structure. 
=peptide.pdb The MOLINFO action with label 
WHOLEMOLECULES ENTITY0the atoms that make up a molecule that you wish to align. 
=1-111 The WHOLEMOLECULES action with label 
jhan: JCOUPLING ...
   TYPEcompulsory keyword 
Type of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM) =HAN 
   ATOMS1the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling.
=@psi-2 COUPLING1Add an experimental value for each coupling. =-0.49 
   ATOMS2the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling.
=@psi-4 COUPLING2Add an experimental value for each coupling. =-0.54 
   ATOMS3the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling.
=@psi-5 COUPLING3Add an experimental value for each coupling. =-0.53 
   ATOMS4the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling.
=@psi-7 COUPLING4Add an experimental value for each coupling. =-0.39 
   ATOMS5the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling.
=@psi-8 COUPLING5Add an experimental value for each coupling. =-0.39 
   
...The JCOUPLING action with label jhan calculates the following quantities:

 Quantity    Description  
jhan.j-0 the calculated J-coupling  This is the 0th of these quantities
jhan.j-1 the calculated J-coupling  This is the 1th of these quantities
jhan.j-2 the calculated J-coupling  This is the 2th of these quantities
jhan.j-3 the calculated J-coupling  This is the 3th of these quantities
jhan.j-4 the calculated J-coupling  This is the 4th of these quantities
jhan.exp-0 the experimental J-coupling  This is the 0th of these quantities
jhan.exp-1 the experimental J-coupling  This is the 1th of these quantities
jhan.exp-2 the experimental J-coupling  This is the 2th of these quantities
jhan.exp-3 the experimental J-coupling  This is the 3th of these quantities
jhan.exp-4 the experimental J-coupling  This is the 4th of these quantities


jhanst: STATS ARGthe input for this action is the scalar output from one or more other actions. 
=(jhan\.j-.*) PARARGthe input for this action is the scalar output from one or more other actions without
derivatives. 
=(jhan\.exp-.*) The STATS action with label jhanst calculates the following quantities:

 Quantity    Description  
jhanst.sqdevsum the sum of the squared deviations between arguments and parameters
jhanst.corr the correlation between arguments and parameters
jhanst.slope the slope of a linear fit between arguments and parameters
jhanst.intercept the intercept of a linear fit between arguments and parameters


PRINT ARGthe input for this action is the scalar output from one or more other actions. 
=jhanst.*,jhan.* FILEthe name of the file on which to output these quantities 
=COLVAR STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=100 The PRINT action with label

Glossary of keywords and components

Description of components

By default this Action calculates the following quantities. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity	Description
score	the Metainference score
sigma	uncertainty parameter
sigmaMean	uncertainty in the mean estimate
neff	effective number of replicas
acceptSigma	MC acceptance for sigma values
j	the calculated J-coupling

In addition the following quantities can be calculated by employing the keywords listed below

Quantity	Keyword	Description
acceptScale	SCALEDATA	MC acceptance for scale value
acceptFT	GENERIC	MC acceptance for general metainference f tilde value
weight	REWEIGHT	weights of the weighted average
biasDer	REWEIGHT	derivatives with respect to the bias
scale	SCALEDATA	scale parameter
offset	ADDOFFSET	offset parameter
ftilde	GENERIC	ensemble average estimator
exp	COUPLING	the experimental J-coupling

The atoms involved can be specified using

ATOMS

the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling. Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one J-coupling will be calculated for each ATOMS keyword you specify.. You can use multiple instances of this keyword i.e. ATOMS1, ATOMS2, ATOMS3...

Compulsory keywords

NOISETYPE	( default=MGAUSS ) functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
LIKELIHOOD	( default=GAUSS ) the likelihood for the GENERIC metainference model, GAUSS or LOGN
DFTILDE	( default=0.1 ) fraction of sigma_mean used to evolve ftilde
SCALE0	( default=1.0 ) initial value of the scaling factor
SCALE_PRIOR	( default=FLAT ) either FLAT or GAUSSIAN
OFFSET0	( default=0.0 ) initial value of the offset
OFFSET_PRIOR	( default=FLAT ) either FLAT or GAUSSIAN
SIGMA0	( default=1.0 ) initial value of the uncertainty parameter
SIGMA_MIN	( default=0.0 ) minimum value of the uncertainty parameter
SIGMA_MAX	( default=10. ) maximum value of the uncertainty parameter
OPTSIGMAMEAN	( default=NONE ) Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
WRITE_STRIDE	( default=10000 ) write the status to a file every N steps, this can be used for restart/continuation
TYPE	Type of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
DOSCORE	( default=off ) activate metainference
NOENSEMBLE	( default=off ) don't perform any replica-averaging
REWEIGHT	( default=off ) simple REWEIGHT using the ARG as energy
SCALEDATA	( default=off ) Set to TRUE if you want to sample a scaling factor common to all values and replicas
ADDOFFSET	( default=off ) Set to TRUE if you want to sample an offset common to all values and replicas
NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
ARG	the input for this action is the scalar output from one or more other actions. The particular scalars that you will use are referenced using the label of the action. If the label appears on its own then it is assumed that the Action calculates a single scalar value. The value of this scalar is thus used as the input to this new action. If * or . appears the scalars calculated by all the proceeding actions in the input file are taken. Some actions have multi-component outputs and each component of the output has a specific label. For example a DISTANCE action labelled dist may have three components x, y and z. To take just the x component you should use dist.x, if you wish to take all three components then use dist.*.More information on the referencing of Actions can be found in the section of the manual on the PLUMED Getting Started. Scalar values can also be referenced using POSIX regular expressions as detailed in the section on Regular Expressions. To use this feature you you must compile PLUMED with the appropriate flag.. You can use multiple instances of this keyword i.e. ARG1, ARG2, ARG3...
AVERAGING	Stride for calculation of averaged weights and sigma_mean
SCALE_MIN	minimum value of the scaling factor
SCALE_MAX	maximum value of the scaling factor
DSCALE	maximum MC move of the scaling factor
OFFSET_MIN	minimum value of the offset
OFFSET_MAX	maximum value of the offset
DOFFSET	maximum MC move of the offset
REGRES_ZERO	stride for regression with zero offset
DSIGMA	maximum MC move of the uncertainty parameter
SIGMA_MEAN0	starting value for the uncertainty in the mean estimate
SIGMA_MAX_STEPS	Number of steps used to optimise SIGMA_MAX, before that the SIGMA_MAX value is used
TEMP	the system temperature - this is only needed if code doesn't pass the temperature to plumed
MC_STEPS	number of MC steps
MC_CHUNKSIZE	MC chunksize
STATUS_FILE	write a file with all the data useful for restart/continuation of Metainference
SELECTOR	name of selector
NSELECT	range of values for selector [0, N-1]
RESTART	allows per-action setting of restart (YES/NO/AUTO)
A	Karplus parameter A
B	Karplus parameter B
C	Karplus parameter C
SHIFT	Angle shift in radians
COUPLING	Add an experimental value for each coupling. You can use multiple instances of this keyword i.e. COUPLING1, COUPLING2, COUPLING3...

Quantity	Description
jhan.j-0	the calculated J-coupling This is the 0th of these quantities
jhan.j-1	the calculated J-coupling This is the 1th of these quantities
jhan.j-2	the calculated J-coupling This is the 2th of these quantities
jhan.j-3	the calculated J-coupling This is the 3th of these quantities
jhan.j-4	the calculated J-coupling This is the 4th of these quantities
jhan.exp-0	the experimental J-coupling This is the 0th of these quantities
jhan.exp-1	the experimental J-coupling This is the 1th of these quantities
jhan.exp-2	the experimental J-coupling This is the 2th of these quantities
jhan.exp-3	the experimental J-coupling This is the 3th of these quantities
jhan.exp-4	the experimental J-coupling This is the 4th of these quantities

Quantity	Description
jhanst.sqdevsum	the sum of the squared deviations between arguments and parameters
jhanst.corr	the correlation between arguments and parameters
jhanst.slope	the slope of a linear fit between arguments and parameters
jhanst.intercept	the intercept of a linear fit between arguments and parameters