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Solvate

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

Input:
- 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)

Output:
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.