Anisotropic Network Model

Files for this example can be downloaded from here. This example is located in mdtoolbox_example/anm_lys/.

Normal mode analysis of ANM

Normal mode analysis of Ca-based anisotropic network model of T4 lysozyme (script_anm.m).

%% Nomal mode analysis of anisotropic network model of T4 lysozyme

% read Ca coordinates from PDB file
[pdb, crd] = readpdb('lys.pdb');
index_ca = selectname(pdb.name, 'CA');
crd = crd(to3(index_ca));
crd = decenter(crd);

% normal mode of anisotropic network model (ANM)
[emode, frequency, covar, covar_atom] = anm(crd, 8.0);

% plot root-mean-square-fluctuations (RMSF)
plot(diag(covar_atom));
axis tight;
xlabel('residue','fontsize',40);
ylabel('variances [a.u.]','fontsize',40);
formatplot
exportas('rmsf');

% plot covariance
imagesc(covar_atom);
axis xy; axis square;
xlabel('residue','fontsize',40);
ylabel('residue','fontsize',40);
colorbar;
formatplot2
exportas('covar_atom');

% export NMD file for visalizing mode structures
writenmd('anm.nmd', crd, emode);

% save data
save script_anm.mat;
rmsf covariance

Visualize mode structures by using the Normal mode wizard in VMD.

$ vmd
vmd > nmwiz load anm.nmd
mode1

Transformation of frame

Transform from the Eckart frame to a non-Eckart frame (script_transformframe.m).

%% Transform from the Eckart frame to a non-Eckart frame.

% load data
load script_anm.mat;

% transform frame
index_fixeddomain = [1:11 77:164]; %atom-index for the larger domain
external_mode = emode(:,(end-5):end);
[emode2, variances2, covar2, covar2_atom] = transformframe(index_fixeddomain, external_mode, covar);

% plot root-mean-square-fluctuations (RMSF)
plot(diag(covar2_atom));
axis tight;
xlabel('residue','FontSize',40);
ylabel('variance [a.u.]','FontSize',40);
formatplot
exportas('rmsf_ne');

% plot covariance
imagesc(covar2_atom);
axis xy; axis square;
xlabel('residue','FontSize',40);
ylabel('residue','FontSize',40);
colorbar;
formatplot2;
exportas('covar_atom_ne');

% export PDB files for visalizing mode structures
writenmd('anm_ne.nmd', crd, emode2);

% save data
save script_transformframe.mat;
rmsf2 covariance2

Visualize mode structures by using the Normal mode wizard in VMD.

$ vmd
vmd > nmwiz load anm_ne.nmd
mode2