GNM

The most recent GNM/ANM source code can be found here:

http://ignmtest.ccbb.pitt.edu/anmdocs/source.html

If you find it useful in your research, please reference the relevant (i)GNM papers in your publication

 

Output File Descriptions
Filename Description
(PDB Code).bfactor This file is the theoretical and experimental B-factor (temperature factor) file and contains three columns. The first column is the residue index, the second is GNM calculated theoretical B-factors and the last column is the x-ray crystallographic b-factors taken from the PDB file.
(PDB Code).ca Experimental data. 5 columns, comprising residue indices, x-, y- and z- coordinates of alpha-carbons, and corresponding temperature factors.
(PDB Code).cc The file contains the cross-correlations between residue fluctuations. The values are between +1(perfect concerted motion) and -1(perfect anti-correlated motions).
(PDB Code).cont It lists the number of neighbors are in contact with a specific residue within a cutoff 7.3Å
(PDB Code).eigen This lists N-1 eigenvalues in the decreasing order
(PDB Code).sloweigenvectors 22 columns. The first column refers to residue indices. Columns 3-22 are the elements of eigenvectors associated with the 20 slowest (lowest frequency) modes, starting from the slowest (first) mode (column 3). The dimension of each element in these vectors is Angstroms.
(PDB Code).fasteigenvectors 22 columns. The first column refers to residue indices, columns 3-22 are the elements of eigenvectors associated with the 20 fastest (highest frequency) modes, starting from the highest mode (column 3) . The dimension of each element in these vectors is Angstroms.
(PDB Code).slowmodes 22 columns. The first column refers to residue indices, columns 3-22 are slow mode shapes associated with the 20 slowest (lowest frequency) modes, starting from the slowest (first) mode. The dimension in each row of columns 3-22 is in Angstrom square, giving the fluctuations resulting from these independent modes.
(PDB Code).fastmodes 22 columns. The first column refers to residue indices, columns 3-22 are fast mode shapes associated with the 20 fastest (highest frequency) modes, starting from the highest mode. The dimension in each row of columns 3-22 is in Angstrom square, giving the fluctuations resulting from these independent modes. Since the last modes reflect localized fast motions in the protein, these modes have few non-zero elements.
(PDB Code).slowav 2 columns. The first column refers to residue indices, column 2 is the residue mean-square fluctuations driven by the joint contribution of the slowest two modes.
(PDB Code).fast10av 3 columns. The first column refers to residue indices, column 2 lists the residue mean-square fluctuations driven by the highest frequency mode, column 3 shows the result from the weighted contribution of the fastest modes.

In order to visualize the output files, open them in a graphing or visualization program and set the indices and axes appropriately. (We use Kalediograph and Microsoft Excel most commonly for this purpose).