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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:
  • Ion number (mol.L-1):
  • Charge density (e.mol.L-1):
  • Water density:

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 APBS 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 dipole moment of 2.35 Debye corresponds to epsilon=19.5 for the solvent. 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 PyMol:
    untar the map.tar file, rename the .cns files into .xplor files and use load and isomesh commands in pymol to load the maps. See Pymol wiki here.

  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 18:25 May 12, 2017.