CS2BACKBONE
This is part of the isdb module

Calculates the backbone chemical shifts for a protein.

The functional form is that of CamShift [68]. The chemical shift of the selected nuclei can be saved as components. Alternatively one can calculate either the CAMSHIFT score (useful as a collective variable [54] or as a scoring function [103]) or a METAINFERENCE score (using DOSCORE). For these two latter cases experimental chemical shifts must be provided.

CS2BACKBONE calculation can be relatively heavy because it often uses a large number of atoms, it can be run in parallel using MPI and OpenMP.

As a general rule, when using CS2BACKBONE or other experimental restraints it may be 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 completely included in ATOMS and a TEMPLATE pdb file for the same atoms should be provided as well in the folder DATADIR. The system is made automatically whole unless NOPBC is used, in particular if the system is made by multiple chains it is usually better to use NOPBC and make the molecule whole WHOLEMOLECULES selecting an appropriate order of the atoms. The pdb file is needed to the generate a simple topology of the protein. For histidine residues 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. Termini groups like ACE or NME should be removed from the TEMPLATE pdb because they are not recognized by CS2BACKBONE.

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), add only the files for the nuclei you need, but each file should include all protein residues. 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 match that used in the pdb file, but must be positive, so double check the pdb. The first and last residue of each chain should be preceded by a # character.

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

The default behavior 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 back-calculated values, where # includes a chain and residue number.

One additional file is always needed in the folder DATADIR: camshift.db. This file includes all the parameters needed to calculate the chemical shifts and can be found in regtest/isdb/rt-cs2backbone/data/ .

Additional material and examples can be also found in the tutorial ISDB: setting up a Metadynamics Metainference simulation as well as in the cs2backbone regtests in the isdb folder.

Examples

In this first example the chemical shifts are used to calculate a collective variable to be used in NMR driven Metadynamics [54] :

Click on the labels of the actions for more information on what each action computes
tested on master
#SETTINGS AUXFOLDER=regtest/isdb/rt-cs2backbone/data
whole: GROUP 
ATOMS
the numerical indexes for the set of atoms in the group.
=2612-2514:-1,961-1:-1,2466-962:-1,2513-2467:-1 WHOLEMOLECULES
ENTITY0
the atoms that make up a molecule that you wish to align.
=whole cs: CS2BACKBONE
ATOMS
The atoms to be included in the calculation, e.g.
=1-2612
DATADIR
compulsory keyword ( default=data/ ) The folder with the experimental chemical shifts.
=data/
TEMPLATE
compulsory keyword ( default=template.pdb ) A PDB file of the protein system.
=template.pdb
CAMSHIFT
( default=off ) Set to TRUE if you to calculate a single CamShift score.
NOPBC
( default=off ) ignore the periodic boundary conditions when calculating distances
metad: METAD
ARG
the input for this action is the scalar output from one or more other actions.
=cs
HEIGHT
the heights of the Gaussian hills.
=0.5
SIGMA
compulsory keyword the widths of the Gaussian hills
=0.1
PACE
compulsory keyword the frequency for hill addition
=200
BIASFACTOR
use well tempered metadynamics and use this bias factor.
=10 PRINT
ARG
the input for this action is the scalar output from one or more other actions.
=cs,metad.bias
FILE
the name of the file on which to output these quantities
=COLVAR
STRIDE
compulsory keyword ( default=1 ) the frequency with which the quantities of interest should be output
=100

In this second example the chemical shifts are used as replica-averaged restrained as in [33] [34] .

Click on the labels of the actions for more information on what each action computes
tested on master
#SETTINGS AUXFOLDER=regtest/isdb/rt-cs2backbone/data NREPLICAS=2
cs: CS2BACKBONE 
ATOMS
The atoms to be included in the calculation, e.g.
=1-174
DATADIR
compulsory keyword ( default=data/ ) The folder with the experimental chemical shifts.
=data/ encs: ENSEMBLE
ARG
the input for this action is the scalar output from one or more other actions.
=(cs\.hn-.*),(cs\.nh-.*) stcs: STATS
ARG
the input for this action is the scalar output from one or more other actions.
=encs.*
SQDEVSUM
( default=off ) calculates only SQDEVSUM
PARARG
the input for this action is the scalar output from one or more other actions without derivatives.
=(cs\.exphn-.*),(cs\.expnh-.*) RESTRAINT
ARG
the input for this action is the scalar output from one or more other actions.
=stcs.sqdevsum
AT
compulsory keyword the position of the restraint
=0
KAPPA
compulsory keyword ( default=0.0 ) specifies that the restraint is harmonic and what the values of the force constants on each of the variables are
=0
SLOPE
compulsory keyword ( default=0.0 ) specifies that the restraint is linear and what the values of the force constants on each of the variables are
=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 .

Click on the labels of the actions for more information on what each action computes
tested on master
#SETTINGS AUXFOLDER=regtest/isdb/rt-cs2backbone/data
cs: CS2BACKBONE 
ATOMS
The atoms to be included in the calculation, e.g.
=1-174
DATADIR
compulsory keyword ( default=data/ ) The folder with the experimental chemical shifts.
=data/
SIGMA_MEAN0
could not find this keyword
=1.0
DOSCORE
( default=off ) activate metainference
csbias: BIASVALUE
ARG
the input for this action is the scalar output from one or more other actions.
=cs.score PRINT
ARG
the input for this action is the scalar output from one or more other actions.
=(cs\.hn-.*),(cs\.nh-.*)
FILE
the name of the file on which to output these quantities
=CS.dat
STRIDE
compulsory keyword ( default=1 ) the frequency with which the quantities of interest should be output
=1000 PRINT
ARG
the input for this action is the scalar output from one or more other actions.
=cs.score
FILE
the name of the file on which to output these quantities
=BIAS
STRIDE
compulsory 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
ha the calculated Ha hydrogen chemical shifts
hn the calculated H hydrogen chemical shifts