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 ADDCOUPLINGS flag and 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 .

- Description of components

The names of the components in this action can be customized by the user in the actions input file. However, in addition to the components that can be customized the following quantities will always be output

Quantity | Description |

sigma | uncertainty parameter |

sigmaMean | uncertainty in the mean estimate |

acceptSigma | MC acceptance |

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 |

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 | ADDCOUPLINGS | 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 |

ADDCOUPLINGS | ( default=off ) Set this flag if you want to have fixed components with the experimental values. |

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 |

TEMP | the system temperature - this is only needed if code doesn't pass the temperature to plumed |

MC_STEPS | number of MC steps |

MC_STRIDE | MC stride |

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... |

- 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.

#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb MOLINFO MOLTYPE=protein STRUCTURE=peptide.pdb WHOLEMOLECULES ENTITY0=1-111 JCOUPLING ... ADDCOUPLINGS TYPE=HAN ATOMS1=@psi-2 COUPLING1=-0.49 ATOMS2=@psi-4 COUPLING2=-0.54 ATOMS3=@psi-5 COUPLING3=-0.53 ATOMS4=@psi-7 COUPLING4=-0.39 ATOMS5=@psi-8 COUPLING5=-0.39 LABEL=jhan ... JCOUPLING jhanst: STATS ARG=(jhan\.j_.*) PARARG=(jhan\.exp_.*) PRINT ARG=jhanst.*,jhan.* FILE=COLVAR STRIDE=100