Gaussian Network Model

Perform Gaussian network model (GNM) based normal mode analysis (NMA) for a protein structure.

gnm(x, ...)

# S3 method for pdb
gnm(x, inds = NULL, temp = 300, keep = NULL,
  outmodes = NULL, gamma = 1, cutoff = 8, check.connect = TRUE, ...)

# S3 method for pdbs
gnm(x, fit = TRUE, full = FALSE, subspace = NULL,
  rm.gaps = TRUE, gc.first = TRUE, ncore = NULL, ...)

Arguments

x

an object of class pdb as obtained from function read.pdb.
...

(in gnm.pdbs) additional arguments passed to gnm.pdb.
inds

atom and xyz coordinate indices obtained from atom.select that selects the elements of pdb upon which the calculation should be based. If not provided the function will attempt to select all calpha atoms automatically.
temp

numerical, temperature for which the amplitudes for scaling the atomic displacement vectors are calculated. Set ‘temp=NULL’ to avoid scaling.
keep

numerical, final number of modes to be stored. Note that all subsequent analyses are limited to this subset of modes. This option is useful for very large structures and cases where memory may be limited.
outmodes

atom indices as obtained from atom.select specifying the atoms to include in the resulting mode object.
gamma

numerical, global scale of the force constant.
cutoff

numerical, distance cutoff for pair-wise interactions.
check.connect

logical, if TRUE check chain connectivity.
fit

logical, if TRUE C-alpha coordinate based superposition is performed prior to normal mode calculations.
full

logical, if TRUE return the complete, full structure, ‘nma’ objects.
subspace

number of eigenvectors to store for further analysis.
rm.gaps

logical, if TRUE obtain the hessian matrices for only atoms in the aligned positions (non-gap positions in all aligned structures). Thus, gap positions are removed from output.
gc.first

logical, if TRUE will call gc() first before mode calculation for each structure. This is to avoid memory overload when ncore > 1.
ncore

number of CPU cores used to do the calculation.

Value

Returns an object of class ‘gnm’ with the following components:

force.constants

numeric vector containing the force constants corresponding to each mode.

fluctuations

numeric vector of atomic fluctuations.

U

numeric matrix with columns containing the raw eigenvectors.

L

numeric vector containing the raw eigenvalues.

xyz

numeric matrix of class xyz containing the Cartesian coordinates in which the calculation was performed.

temp

numerical, temperature for which the amplitudes for scaling the atomic displacement vectors are calculated.

triv.modes

number of trivial modes.

natoms

number of C-alpha atoms.

call

the matched call.

Details

This function builds a Gaussian network model (an isotropic elastic network model) for C-alpha atoms and performs subsequent normal mode analysis (NMA). The model employs a distance cutoff for the network construction: Atom pairs with distance falling within the cutoff have a harmonic interaction with a uniform force constant; Otherwise atoms have no interaction. Output contains N-1 (N, the number of residues) non-trivial modes (i.e. the degree of freedom is N-1), which can then be used to calculate atomic fluctuations and covariance.

Author

Xin-Qiu Yao & Lars Skjaerven

References

Bahar, I. et al. (1997) Folding Des. 2, 173.

See also

gnm.pdbs

Examples

   ## Fetch stucture
   pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )
   
   ## Calculate normal modes
   modes <- gnm(pdb)
   
   ## Print modes
   print(modes)

#> 
#> Call:
#>   gnm.pdb(x = pdb)
#> 
#> Class:
#>   EnergeticModes (gnm)
#> 
#> Number of modes:
#>   129 (1 trivial)
#> 
#> Force constants:
#>   Mode 2: 	0.342
#>   Mode 3: 	0.804
#>   Mode 4: 	1.108
#>   Mode 5: 	1.277
#>   Mode 6: 	1.416
#>   Mode 7: 	1.617
#> 
#> + attr: force.constants, fluctuations, U, L, xyz, temp,
#>         triv.modes, natoms, call
   
   ## Plot modes
   plot(modes)