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· Force field methods
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  · Gromacs NMA
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Gromacs NMA

To calculate force field-based normal modes we need to create an accurate Gromacs topology for the molecule, using the Gromos96 vacuum parameter set. This will ONLY work if all heavy atoms are correctly present in your structure (polar hydrogens are added). If you get an error message, please run your structure through the PDB fixer first.

Currently, this only supports proteins.

To limit server load and memory usage you can only submit structures up to 2000 atoms after adding polar hydrogens (about 1500 heavy atoms). If your structure is larger, try the elastic network modes or download gromacs and run it locally.

Your email adress: (Recommended, for notification)

Job title: (Only alphanumerical characters)

PDB file to calculate modes for:
Max 2000 atoms after adding hydrogens!

Number of normal modes to calculate: (Max 100)
(The first six are translation and rotation.)

Temperature to use for mode amplitudes:
(Motions at 300K are usually very small)

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 are in the file will be used for the calculation. The length of each mode vector will be 3*natoms. It is better not to include Hydrogen atoms in the PDB file.

  • A cutoff is used in the mode calculation. Interactions are shifted, such that both coulomb and VdW potentials reach 0 at the cutoff.

  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 23:55 January 29, 2006.