Normal mode calculation and visualisation

Output
There will be one output PDB file per mode, named mode_#.pdb, directly loadable by PyMol or VMD: this is a concatenation of 30 PDB files separated by an ENDMDL card. This PDB file maybe split into 30 pieces for Molecular Replacement. There is also a tarred file with all modes.
Bonus
As a bonus, you will get a file loadable by Pymol to generate a picture of the Elastic Net associated to your protein 1GGG.pymol (thanks to Patrice Koehl).
Finally, there will be the modes.dat file that contains, for each mode, its frequency and eigenvector list, for your personal use.

Input data formats

• The job title is just for your own identification, but note that it will show up in the public job queue (but your results will not be public).


• The coordinate file should be in PDB format, with only a single structure (no multiple models). Atoms marked with alternate residue flags will be removed. Whatever atoms (ATOM card) are in the file will be used for the calculation (but not the HETATM ones). The length of each mode vector will be 3*natoms.
  It is not recommanded to include Hydrogen atoms in the PDB file.


• All interactions are weighted by exp(-(d_ij(0)/d_0)^2), where d_0 is a distance-weight parameter. This effectively introduces a smoother "cutoff" value than in the original Tirion model. A value of 3.0 Angstrom works well for CA-only models, but you might prefer a larger value (5.0-10.0 Angstrom) for all-atom structures. See the Hinsen article in the References section.


• A cutoff is used in the mode calculation. In the Tirion model (Elastic Network Model) only those pairs of atoms that are closer than the cutoff are linked by a spring of universal length. Ideally this should be choosen so that the weighting causes the interactions to be negligible outside the cutoff, but in practice a cutoff around 10 Angstrom works fine in almost all cases. In general you might be able to use a smaller cutoff value for all-atom calculations than CA-only calculation. See the Tirion article in the References section.


• You can choose how many modes to calculate. The execution time for the sparse matrix solver is more or less proportional to the number of modes requested, while the full matrix solver execution is dominated by the reduction to tridiagonal form - the actual mode calculation is very fast in that case. Due to the memory requirements you cannot use the full solver for more than about 5000 atoms, and the sparse solver is much faster even for small systems (from about 500 atoms) if you only want the first (lowest-frequency) 10-100 modes. Remember that the first six modes correspond to rigid body motions (translation and rotation), so the structurally interesting ones begin at 7.
  You should check in the log file that the first 6 modes have an eigenvalue close to zero.


• If you really want to you can override the automatic choice and specify either the sparse or full solver. Be aware that the full solver wont work for more than 5000 atoms, but it is faster for small systems or if you want a large number of mode vectors (or if you wanted a huge cutoff for some reason).


• Some timing examples for 1ANF with 2860 atoms (Hessian dimension is 8580 by 8580): Calculating 20 modes takes 33 seconds and for 100 modes it increases to 1 minute and 40 seconds.