Build polar H atoms & assign partial charges in a PDB file
This step is necessary for electrostatic calculations using Poisson-Boltzmann solvers etc...
The program does not know how to handle HETATM cards or ligands in general; these atoms will be ignored.
Here partial charges are assigned according to Charmm22 parameters.
The default pH is pH 7.0. Ionisation state of His can be controlled with HSE and HSP residue names.
Atomic radii are taken from the PARSE data set (Sitkoff et al., J. Phys. Chem., 1994, 98:1978-88).
N.B. The output format is the PQR format, which is needed for all AquaSol calculations!
Alternative conformations of side-chains etc... should be removed by the user prior to submission.
You must choose between a Protein PDB file or a nucleic acid PDB file (DNA or RNA).
If you want to submit a job with a protein-nucleic acid complex, you must charge separately the protein file and the nucleic acid file,
then concatenate the two charged PDB files before going to the next step (solve GPBLE).
For more advanced options you should use PDP2PQR server.
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 written and stored for 2 weeks. You can
do without it and write 'nothanks' if you like.
- 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 SHOULD BE removed by the user.
- FAQs: The program will crash if the PDB file contains OT1 and OT2 atoms for the carboxy terminal group. Instead, it needs an O atom
(and optionally an OT atom, but this will be reconstructed anyway).
- N.B. The (output) PQR format is simply a PDB file where Radii are written in the B-factor column
while the Occup. column is assigned to the partial charges.