· Delarue web servers
· PDB_Hydro Flow chart
· Modify PDB structures
  · Fix missing side chains
  · Flip HNQ side chains
  · Refine sidechain torsions
  · Single point mutations
  · Change sequence (decorate)
  · Generate missing loops
· Solvate PDB structures
  · Assign charges (PQR)
  · Run AquaSol
· References
· Homes/Links
· Job queue status

Solvate with AquaSol

Major improvements on both the method and its efficiency have been made on PDB_HYDRO, leading to a new version of the program: AquaSol, thanks to Patrice Koehl (Ref).

The main result of this program is a solvent density map that takes into account electrostatic interactions between the solute charges, the solvent charges and the solvent itself, treated as an assembly of orientable dipoles (Langevin dipoles).
Density maps for free ions and counter ions are also available.

To visualize the maps (ion densities, electrostatic potential), untar the map.tar file, rename the .cns files into .xplor files and use load and isomesh (help here) commands in Pymol to load the maps...

It is also possible to account for water-water interactions in the same formalism as shown here.

  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 11:02 May 02, 2017.