CS2BACKBONE
This is part of the isdb module

Calculates the backbone chemical shifts for a protein.

The functional form is that of CamShift [55]. The chemical shifts of the selected nuclei/residues are saved as components. Reference experimental values can also be stored as components. The two sets of components can then be used to calculate either a scoring function as in [76] [47], using the keyword CAMSHIFT or to calculate ensemble averaged chemical shift as in [29] [30] (see ENSEMBLE, STATS and RESTRAINT). Finally they can also be used as input for METAINFERENCE, [16] . In the current implementation there is no need to pass the data to METAINFERENCE because CS2BACKBONE can internally enable Metainference using the keywork DOSCORE.

CamShift calculation is relatively heavy because it often uses a large number of atoms, in order to make it faster it is currently parallelised with OpenMP.

As a general rule, when using CS2BACKBONE or other experimental restraints it is better to increase the accuracy of the constraint algorithm due to the increased strain on the bonded structure. In the case of GROMACS it is safer to use lincs-iter=2 and lincs-order=6.

In general the system for which chemical shifts are calculated must be completly included in ATOMS and a TEMPLATE pdb file for the same atoms should be provided as well in the folder DATADIR. The atoms are made automatically whole unless NOPBC is used, in particular if the system is made of by multiple chains it is usually better to use NOPBC and make the molecule whole WHOLEMOLECULES selecting an appropriate order.

In addition to a pdb file one needs to provide a list of chemical shifts to be calculated using one file per nucleus type (CAshifts.dat, CBshifts.dat, Cshifts.dat, Hshifts.dat, HAshifts.dat, Nshifts.dat), all the six files should always be present. A chemical shift for a nucleus is calculated if a value greater than 0 is provided. For practical purposes the value can correspond to the experimental value. Residues numbers should go from 1 to N irrespectively of the numbers used in the pdb file. The first and last residue of each chain should be preceeded by a # character. Termini groups like ACE or NME should be removed from the PDB.

CAshifts.dat:
#1 0.0
2 55.5
3 58.4
.
.
#last 0.0
#last+1 (first) of second chain
.
#last of second chain

The default behaviour is to store the values for the active nuclei in components (ca_#, cb_#, co_#, ha_#, hn_#, nh_# and expca_#, expcb_#, expco_#, expha_#, exphn_#, exp_nh#) with NOEXP it is possible to only store the backcalculated values.

A pdb file is needed to the generate a simple topology of the protein. For histidines in protonation states different from D the HIE/HSE HIP/HSP name should be used. GLH and ASH can be used for the alternative protonation of GLU and ASP. Non-standard amino acids and other molecules are not yet supported, but in principle they can be named UNK. If multiple chains are present the chain identifier must be in the standard PDB format, together with the TER keyword at the end of each chain.

One more standard file is also needed in the folder DATADIR: camshift.db. This file includes all the CamShift parameters and can be found in regtest/isdb/rt-cs2backbone/data/ .

All the above files must be in a single folder that must be specified with the keyword DATADIR.

Additional material and examples can be also found in the tutorial Belfast tutorial: NMR restraints

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 these customizable components the following quantities will always be output

Quantity Description
sigma uncertainty parameter
sigmaMean uncertainty in the mean estimate
acceptSigma MC acceptance
ha the calculated Ha hydrogen chemical shifts
hn the calculated H hydrogen chemical shifts
nh the calculated N nitrogen chemical shifts
ca the calculated Ca carbon chemical shifts
cb the calculated Cb carbon chemical shifts
co the calculated C' carbon chemical shifts
expha the experimental Ha hydrogen chemical shifts
exphn the experimental H hydrogen chemical shifts
expnh the experimental N nitrogen chemical shifts
expca the experimental Ca carbon chemical shifts
expcb the experimental Cb carbon chemical shifts
expco the experimental C' carbon chemical shifts

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 wrt the bias
scale SCALEDATA scale parameter
offset ADDOFFSET offset parameter
ftilde GENERIC ensemble average estimator
The atoms involved can be specified using
ATOMS The atoms to be included in the calculation, e.g. the whole protein.. For more information on how to specify lists of atoms see Groups and Virtual Atoms
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=1000 ) write the status to a file every N steps, this can be used for restart/continuation
DATADIR ( default=data/ ) The folder with the experimental chemical shifts.
TEMPLATE ( default=template.pdb ) A PDB file of the protein system to initialise ALMOST.
NEIGH_FREQ ( default=20 ) Period in step for neighbour list update.
NRES Number of residues, corresponding to the number of chemical shifts.
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
CAMSHIFT ( default=off ) Set to TRUE if you to calculate a single CamShift score.
NOEXP

( default=off ) Set to TRUE if you don't want to have fixed components with the experimetnal 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 proceding 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 componets 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
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 doesnt' 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 usefull 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)

Examples

In this first example the chemical shifts are used to calculate a scoring function to be used in NMR driven Metadynamics [47] :

whole: GROUP ATOMS=2612-2514:-1,961-1:-1,2466-962:-1,2513-2467:-1
WHOLEMOLECULES ENTITY0=whole
cs: CS2BACKBONE ATOMS=1-2612 NRES=176 DATADIR=../data/ TEMPLATE=template.pdb CAMSHIFT NOPBC
metad: METAD ARG=cs HEIGHT=0.5 SIGMA=0.1 PACE=200 BIASFACTOR=10
PRINT ARG=cs,metad.bias FILE=COLVAR STRIDE=100

In this second example the chemical shifts are used as replica-averaged restrained as in [29] [30].

cs: CS2BACKBONE ATOMS=1-174 DATADIR=data/ NRES=13
encs: ENSEMBLE ARG=(cs\.hn_.*),(cs\.nh_.*)
stcs: STATS ARG=encs.* SQDEVSUM PARARG=(cs\.exphn_.*),(cs\.expnh_.*)
RESTRAINT ARG=stcs.sqdevsum AT=0 KAPPA=0 SLOPE=24

PRINT ARG=(cs\.hn_.*),(cs\.nh_.*) FILE=RESTRAINT STRIDE=100

This third example show how to use chemical shifts to calculate a METAINFERENCE score .

cs: CS2BACKBONE ATOMS=1-174 DATADIR=data/ NRES=13 DOSCORE NDATA=24
csbias: BIASVALUE ARG=cs.score

PRINT ARG=(cs\.hn_.*),(cs\.nh_.*) FILE=CS.dat STRIDE=1000
PRINT ARG=cs.score FILE=BIAS STRIDE=100