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Your email adress: (Recommended, for notification)

Job title: (Only alphanumerical characters - no space)

PDB file (with partial charges) in APBS style Ex: PQR
Use internal facility (Assign charges) or the Pdb2pqr server

Input parameters

Number of grid points (2N+1) along each axis:

Grid size: (Angströms)

Solvent info

  • Solvent size (diameter): (Angströms)
  • Dipole moment: (Debye)
  • Concentration: (Mol.L-1)
  • Add dipole-dipole interactions?   

Salt info

  • Monovalent cation concentration: (Mol.L-1)
  • Monovalent anion concentration: (Mol.L-1)
  • Radius (Angströms)
  • Stern region thickness (Angströms)

Surface info

  • Surface type

  • Probe radius: (Angströms)

Method info

  • Elliptic equation

  • Boundary condition

Output parameters

Map format

Output maps

  • Electrostatic potential (kT/e):
  • (Signed) Ion concentration (mol.L-1):
  • (Signed) Charge density (e.mol.L-1):
  • Water density (mol.L-1):

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: this is actually what is called the PQR format.
    N.B. Learn more about the APBS format here!

  • 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 dipole moment of 2.35 Debye corresponds to epsilon=19.5 for the solvent. This is the default value as this is the physical one for water. The scale law is such that epsilon is proportional to the square of p_0.

Output data formats

  • To visualize the CNS/Xplor maps (ion densities, electrostatic potential) you can use either
    First you need to save on your disk and untar the maps.tar file by typing
    $ untar xvf maps.tar

    For Pymol it is best to rename the .cns files into .xplor files and use load and isomesh commands in pymol to load the maps. See Pymol wiki here.
    For Coot, make sure you load the map as a difference map to contour both positive and negative ions.
    In both cases, you need to save the mol_center.pqr file, because the map is contoured around this recentered molecule.

  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 14:20 October 19, 2018.