Solvate a PDB file

This web-server solves a Generalized Poisson-Boltzmann Equation, where the solvent is represented as an assembly of Langevin dipoles of finite size and variable density, orienting themselves in the electrostatic field of a (fixed) macromolecule (the solute), in the presence of free ions of given concentration.
All species are put on a grid to treat the size-exclusion problem. The equation is solved using the multi-grid method.
This is the work of Cyril Azuara for his Ph.D. thesis, using formalism developed in collaboration with Henri Orland (IPhT, CEA, Saclay, France) in 2005-2008.
This web site is fully described in the following publication (NAR Web server issue).

A full description of the method has been published shortly afterwards in Biophys. J (2008).

The program has actually been accelerated by a factor of 20 in AquaSol by Patrice Koehl (see Menu on the left).
If you are interested in getting the code, please contact either Koehl@cs.ucdavis.edu or marc.delarue@pasteur.fr.

Constructing polar hydrogen atoms and assigning partial charges can be done on line using the menu on the left.

The dimerization interface is clearly seen as poorly solvated.