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  · Go-like Energy NMA
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NMA with a Go-like Energy Model

Here we use an expanded Energy Model, the so-called Go-model, to calculate the Hessian and the Normal Modes, containing, in addition to the bond length term, two additional elastic terms based on 3-atoms (torsional) and 4-atoms (dihedral) angles, and a non-local-term (vdw + electrostatics).

Vtot = Vbond + Vtor + Vdihed + Vnon-local

References
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Your email adress: (Recommended, for notification)


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


PDB file to be projected Ex: Example


Cutoff used for neighbours definition (Å):

Number of modes to calculate:

Rmsd for output trajectories

Last mode for output trajectories


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.




  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 10:09 May 09, 2017.