Calculates Normal Modes using Go-like Energy Model and Delaunay-defined neighbours for very large PDB files (beta version)

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About this form

This form will submit a Normal Modes calculation on the given input PDB file.

You need at least one pdb file to calculate Normal Modes using variants of the Elastic Network Model. No cutoff is needed if you use the Delaunay tessalation to define neighbours.
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).

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


Here we use an expanded Energy Model, the so-called Go-model, to calculate the Normal Modes. It contains an elastic term on the bond lengths, two elastic terms based on 3-atoms (torsional) and 4-atoms (dihedral) angles, and a non-local-term (vdw-like).

Vtot = Vbond + Vtor + Vdihed + Vnon-local

The neighbours are defined either by Delaunay triangulation (no cutoff) or with a cutoff criterion.

By entering your e-mail address you'll get notified as soon as the calculation completes. A reminder of the URL for accessing the results will be part of the message.

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The task title is your personal reminder for identifying this calculation. It will be displayed in the results page.

Must contain alphanumeric characters only

Please provide the coordinates file for which you want to calculate normal modes. The file should be in PDB format, with only a single structure (no multiple models). Atoms marked as alternate residues, Hydrogen atoms and HETATM records will be ignored.

P.S. The length of each mode vector will be 3×Natoms.

Must contain non-Hydrogen ATOM records 

By selecting CA only, atoms marked as alternate residues, Hydrogen atoms and HETATM records will be ignored.


Format for the output file. For files with more than 50 chains, use mmCIF.

Mode number that you want to calculate (larger than 6). For the moment we authorize only one mode per submission, as these files might be huge.

Must be an integer in the range of 7 to 106

Go energy should be used ONLY for CA-only models!


How do you want to define neighbours in the pairwise Energy terms?

Must be a number greater than 1

K_ij: A rule of thumb is that k × cutoff2 ≈ 10 kcal/Mol
Leave as is for Delaunay neighbors definition.
RMSD: this option defines the mean rmsd of atoms that you want for this mode (i.e. it is equivalent to a temperature).

= Must be a number greater than 0.1 = Must be a number greater than or equal to 0