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  · All in one
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Solvate all in one go

This will successively:
- Add charges to protein PDB file (but not missing side chains!)
- Call the Generalized Poisson-Boltzmann-Langevin solver
- Place water molecules at preferential hydration sites.

Details of the method can be found in here and here.
The program will ajust the grid size such that there is at least 14. Angstrom (two Bjerrum lengths at 300K in the solvent) between the surface of the solute and the border of the grid.
For 65 grid points, the program will take about 5 mn cpu.
For 129 grid points, it will take about an 20 mn of cpu.

Brief description

Input:
- PDB file containing partial charges and atomic radii
- Parameters for grid size, dipole strength and free ions and dipole concentrations and sizes (see below)

Output:
- prot_center.pdb : centered PDB file
- placed_h2o.pdb : PDB file containing the placed water molecules
- sol_zones.pdb : PDB file OK for PyMol representation
Just type:
pymol sol_zones.pdb sol_zones.py (to be found here) and then (in pymol) color_b

Your email adress: (Recommended, for notification)


Job title: (Only alphanumerical characters)


PDB file (partial charges will be added as in here)
Ex: PDB. Works for Protein PDB files only, right now.
For a DNA or a RNA, go to "Build polar hydrogens" option.


Input parameters for Poisson-Langevin Solver


Number of grid points (2^N + 1); solvent/ion size (A)

---

Concentration (M) of free ions
(electroneutrality will be enforced)

Valency of positive free ions (integer)

Valency of negative free ions (integer)

Concentration (M) and dipole moment (D) of solvent
---

Choose of the surface type
   


Input data formats

  • The e-mail address is used to send an e-mail containing the address of the directory where the results will be stored for 15 days. You can do without it and reply 'nothanks' if you want.

  • 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 SHOULD be removed by the user prior to submission. HETATM cards will be ignored.

  • The choice of the surface type: The solvent accessible surface (SAS) corresponds to the Lee and Richards definition (Lee B. and Richards F. M., 1971, J. Mol. Biol., 55 : 379). The molecular surface (MS) corresponds to the calculation of Jiang and Brunger (Jiang J. S. and Brunger A. T., 1994, J. Mol. Biol., 243 : 100). Note that the two surfaces are different only if the number of grid points is 129.

  • The input parameter file is of the form:
    #IGRID ODD= 65
    #SIZE H = 1.0 (Angstr.)
    #RADPRB = 1.4 (Angstr.)
    #R_DIP = 1.4 (Angstr.)
    #R_ION = 1.4 (Angstr.)
    #VALENCE P= 1
    #VALENCE N= 1
    #C_DIP = 55 M
    #C_ION = 0.1 M
    #P0 = 1.85 D
    #SURFACE = 0 (SAS) or 1 (MS)



  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 17:11 May 09, 2016.