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Generalized Poisson-Boltzmann-Langevin solver.
Details of the method can be found in here and and here.
In short, we minimize by the multi-grid method the following free-energy functional:

Brief description

- PDB file containing partial charges and atomic radii as in the PQR format. See the PDB2PQR server for more advanced functions...
- Solvent and ions parameters (see below)

1/ CNS maps to be seen with Pymol (Help) or O:
- phi.xplor : CNS map of electrostatic potential
- dipole.xplor : CNS map of solvant density
- ions.xplor : CNS map of + and - free ions density
- epsilon.xplor: CNS map of epsilon(r)

2/ PDB files:
- prot_center.pdb : centered PDB file with center of mass at 0., 0., 0.
- Efield.pdb : electrostatic field around the protein (loadable with "O")

3/ the log file GPBE.log containing:
- list of inputs parameters
- infos on protein and recentering
- extrema of the electrostatic potential in the solvent region
- free energy of the systeme in kT
- total cpu time

Your email adress: (Recommended, for notification)

Job title: (Only alphanumerical characters - no space)

PDB file (with partial charges) in APBS style Ex: PQR
See the PDB2PQR server!

Input parameters

Number of grid points (2^N + 1)

Radius probe size (left); Solvent and ion size (right)

Concentration (M) of free ions (electroneutrality will be enforced if the positive and negative ions have different valencies)

Valency of positive (left) and negative (right) free ions (integers)

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

Choose 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 will be removed. Charges should be in the B-factors column and atomic radius in the occupation column.
    N.B. This is the PQR format!

  • 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 described by Jiang and Brunger (J. Mol. Biol., 1994, 243: 100).

  • 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 18:18 May 12, 2017.