Action: KENREF
| Module | kenref |
|---|---|
| Description | Usage |
| Restrains an ensemble of replicas against NMR observables (kinetic ensemble refinement). |   |
Details and examples
Restrains an ensemble of replicas against NMR observables (kinetic ensemble refinement).
KENREF computes an NMR observable as an average over the whole ensemble of replicas, compares it with
experimental data, and applies the resulting restraint force to the atoms. Unlike most biases it acts on
coordinates rather than on collective variables, so it takes no ARG.
The energy model is selected by name with MODEL:
MODEL |
restrains |
|---|---|
SIGMA |
cross-relaxation rates (interproton NOE build-up) |
PLATEAUS |
NOE plateau values |
RELAX |
longitudinal / transverse relaxation |
Because the observable is an ensemble average, RELAX needs at least two replicas (run with --multi);
SIGMA and PLATEAUS also work with a single replica.
EXP_DATA_FOLDER holds the experimental data and the atom-pair definitions. ATOMNAME_MAPPING is a PDB
that maps atom names to indices, and is also used as the reference structure when REF is omitted. When
FIT_TO_REFERENCE is set the coordinates are Kabsch-fitted onto the reference, using GUIDE_ATOMS,
before the observable is computed, and the derivatives are rotated back afterwards. SATURATE_FORCES
clamps the resulting force to MAX_FORCE.
The action outputs its restraint energy as .energy (equal to .bias) and, as a diagnostic, the RMSD
from the reference as .rmsd.
This module needs the external KEnRef library and is not compiled by default; see the module documentation for how to build it.
Examples
Restraining a fragment of GB3 against cross-relaxation rates:
#SETTINGS MOLFILE=regtest/kenref/rt-kenref-sigma/gb3_frag.pdb kenref: KENREFRestrains an ensemble of replicas against NMR observables (kinetic ensemble refinement). More details ... MODEL The energy model to use (e=SIGMA K Force constant=1.0 N Power scaling factor=0.25 PROTON_MHZSpectrometer proton field strength in MHz (SIGMA model)=700.0 EXP_DATA_FOLDERFolder with relaxation spectral-density experimental data (RELAX model)=regtest/kenref/rt-kenref-sigma/ REFReference structure PDB for alignment=regtest/kenref/rt-kenref-sigma/gb3_frag.pdbClick here to see an extract from this file.ATOMNAME_MAPPING PDB file with atom-name -> atom-index mapping (also used as reference if REF is omitted)=regtest/kenref/rt-kenref-sigma/gb3_frag.pdbClick here to see an extract from this file.GUIDE_ATOMSAtoms used for alignment to reference=1,5,18,20,22,35,37,39,56,58,60,78,80,82,97 MAX_FORCEMaximum force magnitude (default 9999)=999 FIT_TO_REFERENCE Fit coordinates to reference before calculating energy SATURATE_FORCES Clamp forces to MAX_FORCE ...
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=kenref.bias,kenref.energy,kenref.rmsd FILEthe name of the file on which to output these quantities=colvar
Input
The 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 |
|---|---|---|
| GUIDE_ATOMS | atoms | Atoms used for alignment to reference |
Output components
This action calculates the values in the following table. 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 | Description |
|---|---|---|
| bias | scalar | the instantaneous value of the bias potential |
| energy | scalar | Total KEnRef restraint energy |
| rmsd | scalar | RMSD from reference (after fitting) |
Full list of keywords
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| GUIDE_ATOMS | input | none | Atoms used for alignment to reference |
| MODEL | compulsory | SIGMA | The energy model to use (e |
| K | compulsory | 1.0 | Force constant |
| N | compulsory | 0.25 | Power scaling factor |
| ATOMNAME_MAPPING | compulsory | undefined | PDB file with atom-name -> atom-index mapping (also used as reference if REF is omitted) |
| NUMERICAL_DERIVATIVESThis keyword do not have examples | optional | false | calculate the derivatives for these quantities numerically |
| MAX_FORCE | optional | not used | Maximum force magnitude (default 9999) |
| REF | optional | not used | Reference structure PDB for alignment |
| FIT_TO_REFERENCE | optional | false | Fit coordinates to reference before calculating energy |
| SATURATE_FORCES | optional | false | Clamp forces to MAX_FORCE |
| EXP_DATA_FILEThis keyword do not have examples | optional | not used | Experimental data file with atom1/atom2 pairs and g1/g2 targets (PLATEAUS model) |
| EXP_DATA_FOLDER | optional | not used | Folder with relaxation spectral-density experimental data (RELAX model) |
| RATES_FILEThis keyword do not have examples | optional | not used | CSV file (a_coef |
| PROTON_MHZ | optional | not used | Spectrometer proton field strength in MHz (SIGMA model) |
| RESTARTThis keyword do not have examples | optional | not used | allows per-action setting of restart (YES/NO/AUTO) |
| UPDATE_FROMThis keyword do not have examples | optional | not used | Only update this action from this time |
| UPDATE_UNTILThis keyword do not have examples | optional | not used | Only update this action until this time |