Action: JCOUPLING

Module	isdb
Description	Usage
Calculates 3J coupling constants for a dihedral angle.

Details and examples

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
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein STRUCTUREa file in pdb format containing a reference structure=peptide.pdb
The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-111

JCOUPLINGCalculates 3J coupling constants for a dihedral angle. More details ...
    TYPEType 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-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information.  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-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information.  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-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information.  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-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information.  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-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information.  COUPLING5Add an experimental value for each coupling=-0.39
    LABELa label for the action so that its output can be referenced in the input to other actions=jhan
... JCOUPLING

The JCOUPLING action with label jhan calculates the following quantities: Quantity    Description  
jhan.score the Metainference score
jhan.sigma uncertainty parameter
jhan.sigmaMean uncertainty in the mean estimate
jhan.neff effective number of replicas
jhan.acceptSigma MC acceptance for sigma values
jhan.j the calculated J-couplingjhanst: STATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More details ARGthe labels of the values from which the function is calculated=(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 parametersPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=jhanst.*,jhan.* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=100

Input

The arguments and atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
ARG	scalar	the labels of the values from which the function is calculated
ATOMS	atoms	the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling

Output components

This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Name	Type	Keyword	Description
score	scalar	default	the Metainference score
sigma	scalar	default	uncertainty parameter
sigmaMean	scalar	default	uncertainty in the mean estimate
neff	scalar	default	effective number of replicas
acceptSigma	scalar	default	MC acceptance for sigma values
acceptScale	scalar	SCALEDATA	MC acceptance for scale value
acceptFT	scalar	GENERIC	MC acceptance for general metainference f tilde value
weight	scalar	REWEIGHT	weights of the weighted average
biasDer	scalar	REWEIGHT	derivatives with respect to the bias
scale	scalar	SCALEDATA	scale parameter
offset	scalar	ADDOFFSET	offset parameter
ftilde	scalar	GENERIC	ensemble average estimator
j	scalar	default	the calculated J-coupling
exp	scalar	COUPLING	the experimental J-coupling

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
ARGThis keyword do not have examples	input	none	the labels of the values from which the function is calculated
ATOMS	input	none	the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
NOISETYPEThis keyword do not have examples	compulsory	MGAUSS	functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
LIKELIHOODThis keyword do not have examples	compulsory	GAUSS	the likelihood for the GENERIC metainference model, GAUSS or LOGN
DFTILDEThis keyword do not have examples	compulsory	0.1	fraction of sigma_mean used to evolve ftilde
SCALE0This keyword do not have examples	compulsory	1.0	initial value of the scaling factor
SCALE_PRIORThis keyword do not have examples	compulsory	FLAT	either FLAT or GAUSSIAN
OFFSET0This keyword do not have examples	compulsory	0.0	initial value of the offset
OFFSET_PRIORThis keyword do not have examples	compulsory	FLAT	either FLAT or GAUSSIAN
SIGMA0This keyword do not have examples	compulsory	1.0	initial value of the uncertainty parameter
SIGMA_MINThis keyword do not have examples	compulsory	0.0	minimum value of the uncertainty parameter
SIGMA_MAXThis keyword do not have examples	compulsory	10.	maximum value of the uncertainty parameter
OPTSIGMAMEANThis keyword do not have examples	compulsory	NONE	Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
WRITE_STRIDEThis keyword do not have examples	compulsory	10000	write the status to a file every N steps, this can be used for restart/continuation
TYPE	compulsory	none	Type of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)
NUMERICAL_DERIVATIVESThis keyword do not have examples	optional	false	calculate the derivatives for these quantities numerically
DOSCOREThis keyword do not have examples	optional	false	activate metainference
NOENSEMBLEThis keyword do not have examples	optional	false	don't perform any replica-averaging
REWEIGHTThis keyword do not have examples	optional	false	simple REWEIGHT using the ARG as energy
AVERAGINGThis keyword do not have examples	optional	not used	Stride for calculation of averaged weights and sigma_mean
SCALEDATAThis keyword do not have examples	optional	false	Set to TRUE if you want to sample a scaling factor common to all values and replicas
SCALE_MINThis keyword do not have examples	optional	not used	minimum value of the scaling factor
SCALE_MAXThis keyword do not have examples	optional	not used	maximum value of the scaling factor
DSCALEThis keyword do not have examples	optional	not used	maximum MC move of the scaling factor
ADDOFFSETThis keyword do not have examples	optional	false	Set to TRUE if you want to sample an offset common to all values and replicas
OFFSET_MINThis keyword do not have examples	optional	not used	minimum value of the offset
OFFSET_MAXThis keyword do not have examples	optional	not used	maximum value of the offset
DOFFSETThis keyword do not have examples	optional	not used	maximum MC move of the offset
REGRES_ZEROThis keyword do not have examples	optional	not used	stride for regression with zero offset
DSIGMAThis keyword do not have examples	optional	not used	maximum MC move of the uncertainty parameter
SIGMA_MEAN0This keyword do not have examples	optional	not used	starting value for the uncertainty in the mean estimate
SIGMA_MAX_STEPSThis keyword do not have examples	optional	not used	Number of steps used to optimise SIGMA_MAX, before that the SIGMA_MAX value is used
TEMPThis keyword do not have examples	optional	not used	the system temperature - this is only needed if code doesn't pass the temperature to plumed
MC_STEPSThis keyword do not have examples	optional	not used	number of MC steps
MC_CHUNKSIZEThis keyword do not have examples	optional	not used	MC chunksize
STATUS_FILEThis keyword do not have examples	optional	not used	write a file with all the data useful for restart/continuation of Metainference
FMTThis keyword do not have examples	optional	not used	specify format for HILLS files (useful for decrease the number of digits in regtests)
SELECTORThis keyword do not have examples	optional	not used	name of selector
NSELECTThis keyword do not have examples	optional	not used	range of values for selector [0, N-1]
RESTARTThis keyword do not have examples	optional	not used	allows per-action setting of restart (YES/NO/AUTO)
NOPBCThis keyword do not have examples	optional	false	ignore the periodic boundary conditions when calculating distances
AThis keyword do not have examples	optional	not used	Karplus parameter A
BThis keyword do not have examples	optional	not used	Karplus parameter B
CThis keyword do not have examples	optional	not used	Karplus parameter C
SHIFTThis keyword do not have examples	optional	not used	Angle shift in radians
COUPLING	optional	not used	Add an experimental value for each coupling

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

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