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Place Water Molecules

Using the result of the Generalized Poisson-Boltzmann-Langevin solver, this program places water molecules at preferential sites of hydration.
Details of the method can be found in the following publications: here and and here.

Brief description

Input:
- PDB file containing the centered molecule (prot_center.pdb from GPBL solver)
- TH_DIP.pot file (output from the GPBL solver)
- dipole.cns, the CNS map coming from the GPBL solver.
- Parameters (see below)

Output:
- placed_h2o.pdb, a PDB file containing the water molecules.
- sol_zones.pdb, a PDB file with high or low solvation information to be loaded with PyMol.
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 - no space)


PDB file (centered)


TH_DIP.pot file


Dipole.cns file (map)


Three options are proposed to place water molecules using either:

  • 1: a threshold in the solvent density (compared to the bulk density),
  • 2: the weight (in grams) of water molecules per g of solute (protein),
  • 3: the total number of water molecules needed (by default 1 per residue)

Option (Default is 1)

Input parameters (See below)
--- ---


Input data formats

  • The e-mail address is used to send a message containing the address of the directory where the result is stored. It is not compulsory and you can just write 'nothanks' it will work too.

  • 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.

  • The input parameter file is of the form:
    #CHOIX = 1
    #SEUIL = 1.2
    #HYDLEVEL = 0.4
    #NB WATER = 120



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