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Gromacs energy minimization

This will ONLY work if all heavy atoms are present in your structure, since we need to create a Gromacs topology using the Gromos96 vacuum force field. If you get an error message, please run your structure through the PDB fixer first.

Currently, this only supports proteins.

To limit server load you can only minimize structures with less than 10,000 atoms after adding polar hydrogens (about 7000 heavy atoms). If you need to minimize larger structures you can download Gromacs and run it locally.

Your email adress: (Recommended, for notification)

Job title: (Only alphanumerical characters)

PDB file to minimize (Max 10,000 atoms after adding H's):

Method to use (advanced):

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.

  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 23:36 January 29, 2006.