JCOUPLING
 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
WHOLEMOLECULES ENTITY0the atoms that make up a molecule that you wish to align. =1-111
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 You can use multiple instances of this
keyword i.e. =-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 You can use multiple instances of this
keyword i.e. =-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 You can use multiple instances of this
keyword i.e. =-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 You can use multiple instances of this
keyword i.e. =-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 You can use multiple instances of this
keyword i.e. =-0.39

...
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-.*)
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

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...