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NMA with Delaunay-defined neighbours

Input
You need at least one pdb file to calculate Normal Modes using the Elastic Network Model. No cutoff is needed if you use the Delaunay tessalation.
You can also define the regular ENM with a cutoff, and do NMa in a new version based on Krylov space, written by Patrice Koehl, that accepts structures with a very large number of atoms (e.g. 100,000).

Output
There will be one output PDB file per mode, named traj_mode#.pdb, directly loadable by PyMol or VMD.

Reference
Article_1
Article_2

Your email adress: (Recommended, for notification)


Job title: (Only alphanumerical characters, no space)


PDB file for which you want to calculate modes
(Protein Ex: 1GGG.pdb). N.B. No Hydrogen atoms!
(Nucleic Acids Ex: tRNA.pdb). HETATOM will be ignored!


Number of modes to calculate (Max 106)
(The first six ones are translation and rotation)

Processing the PDB (for proteins or nucleic acids)?
(0 for CA-and-P-only and 1 for all atoms)

Type of Elastic Network
1 for spherical model with cutoff Angstrom
2 for Delaunay tessalation (no parameter)

Last Mode number for the Output Trajectory

Type of Output Trajectory
0 for trajectories at RT with k (kT/A^2)
1 for deformed output files with rms (A)


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.

  • Careful You should carefully check that the first six normal modes have zero (or close to zero) frequency. There should be a clear gap in the frequencies between the sixth and seventh eigen-mode frequency. If not, restart the calculation, this time asking for more Normal Modes. Indeed, this is most probably due to the dimensioning of the Krylov space, which is set to 2*Nmodes. If this Krylov space is too small the program will not do well to distinguish low-frequency modes.

    Options
    Choose the number of modes you want, provided that there are less than 106 (=100+6); that is only to save our disk space: if you want more, please send us an e-mail.
    The scale (amplitude) of the movement can be chosen by controlling the average rmsd of the trajectory.

    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.




  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 12:02 June 22, 2017.