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· Delarue web servers · Nomad Flow-chart · Normal Mode calculation · Examples (Movies) · Submit a job (from PDB file) · Elastic Energy (Perturb. Anal.) · Overlap coefficients · Include Profit step · Molecular Replacement · Split trajectory (for MR) · Generate decoys (MixMod) · X-Ray refinement · Standard refinement · Screening Mol. Repl. Solns. · EM refinement · Documents/Examples · Get Structure Factors · Submit a job (no NCS) · Submit job with NCS · Docking refinement · Submit a job (refinement) · Submit a job (scanning) · Force field methods · Energy minimization · Gromacs NMA · References · Homes/Links · Job queue status |
Gromacs OPLS-AA/L force field Normal mode calculationNormally, we recommend using the elastic network model to calculate normal modes for several reasons:
Gromacs needs to create an all-atom topology of your input structure, so the chains must be whole and no heavy atoms missing. If your structure is not a simple protein you will probably have to download Gromacs yourself (it's available at Gromacs, but you might have to use the CVS version) and manually edit a topology. Hydrogen atoms will be added, as well as charged termini for proteins. Since these jobs are quite a bit more taxing on the server compared to the elastic network models, we limit the system size to 5000 atoms and don't run more than 5000 energy minimization steps. If you install Gromacs locally these limitations are obviously no longer an issue.
The results will be returned both as a raw datafile with normal mode vectors,
and as a series of PDB movies (structures separated by ENDMDL in a single file). If you load these in a program like PyMol you will get a nice visualization of the mode-induced movements. BUT: Please, please, please try the Elastic Network version first - it will likely do everything you need without having to worry about these problems :-) |
Marc Delarue |
http://lorentz.dynstr.pasteur.fr Page last modified 16:06 March 06, 2006. |