PDB Preprocessor

The PDB preprocessor converts a standard PDB file into one that is more easily used as input to AMBER utilities such as tleap.  

It does these things:

  • Checks for possible disulfide bond formation based on distance.  For all possible bonds approved by the user, the processor will change the relevant CYS residues to type CYX per AMBER convention.
  • Checks for, and if found removes, any residues that are not represented in the force field.
  • Checks for unrecognized heavy atoms in residues that are represented in the force field.  If any are found, the utility will not process the pdb file.  The user must modify or remove the conflicting residues.
  • Removes and replaces any hydrogens whose names are not consistent with the force field template for the residue in which they reside.
  • Allows the user to specify chain termination other than the standard zwitterionic configuration (coming soon).
  • Checks for mid-chain missing residues.  If any are found, a TER card is placed at the break point and the user can specify the type of chain termination (default: zwitterionic).
  • Sets histidine residues to their epsilon protonation state.  The user may alter this selection in bulk or on a per-residue basis.

Files available for download:

The standalone PDB Preprocessor provides only an altered PDB file for download.

When accessed as part of the Glycoprotein Builder, users may also download AMBER prmtop and inpcrd files.  They may also solvate the protein or, if the protein is not neutral, add counter ions.  To access these features for an unglycosylated protein, they should simply set the desired options, then choose to “Download Current Structure” without adding any glycans.