· 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 loops
· Solvate PDB structures
· Assign charges (PQR)
· Solvate using GPBL
· Place Waters
· All in one
· NEW !!! AQUASOL !!!
· Run AquaSol
· Job queue status
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.
- 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)
- 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.
pymol sol_zones.pdb sol_zones.py (to be found here) and then (in pymol) color_b
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
- The input parameter file is of the form:
#CHOIX = 1
#SEUIL = 1.2
#HYDLEVEL = 0.4
#NB WATER = 120