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  · Introduction
· Coarse-Graining
  · Protein CG
· Non-constant Kij
  · Hessian Proj. CG
  · Decimation CG
· New NMA Models
  · Go-like Energy NMA
  · Delaunay + classic NMA
· References
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· Distances Bridges

Coarse-grain: projection of Hessian on CA/P atoms

Here we project the Hessian of the classical ENM of an all-atoms model into a CA-only (proteins) or P-only (nucleic acids) ENM model. This redefines the elastic constants between the remaining atoms.
Then the Normal Modes are calculated, with the new Hessian.


Your email adress: (Recommended, for notification)

Job title: (Recommendend, but only alphanumerical characters - no space)

PDB file to be projected Ex: Example

Cutoff for neighbours definition in ENM (Å):

Number of Modes to calculate:

Rmsd for output Trajectory (Å):

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 conformation flags will be removed. Heteroatoms (HETATM) will be copied to the output file.

  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 15:36 May 08, 2017.