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Add Protons to an Existing PDB Structure

pdbUtilNight Add Protons to an Existing PDB Structure

Frank Delaglio delaglio@nih.gov


About the PDB Utility Server to Add H Atoms to an Existing PDB Structure

Description: This server takes as input a PDB file, and creates a new version of the PDB file with all atoms, including both heavy atoms and H atoms. Any H atoms in the input are ignored. By default, the heavy atom coordinates in the new PDB file will be the same as those in the input.

Limitations: Currently, the server only supports PDB files consisting of one or more chains of the common 20 amino acids. In the case of PDB files consisting of multiple chains, the chains must be identified according to the CHAINID column of the PDB input (column 22 of 1 to 80). If the input contains alternative structures with different LOCIDs (column 17), the first one encountered will be used.

How it Works: the server extracts the residue sequence from the input PDB file, and uses this information to create an extended structure with all atoms, both heavy atoms and H atoms. If any residues are missing in the input structure, these are also deleted from the extended structure. The server then uses a conventional simulated annealing protocol to fold the extended structure so that its heavy atom coordinates match those from the input as closely as possible, commonly to better than 0.1 Angstrom. Then, each heavy atom in this refined structure is moved by a small distance back to its exact original coordinates from the input, and any bonded H-atoms are moved accordingly.

PDB Header Information, Atom Numbering, HETATMS: All REMARKs etc. prior to the first ATOM entry in the input are included in the output. Any HETATM entries from the input are appended to the result with their coordinates unchanged. Other trailing entries from the input, such as CONECT records, are not included in the output. The ATOMs and HETATMS in the output are renumbered consecutively starting at 1.

How Long it Takes: On our current server system, the entire procedure takes about one minute for a 100-residue protein when no other jobs are running.

Advanced Options: The server can also be used to help resolve steric clashes in a structure. When used for this purpose, the heavy atom coordinates in the output are allowed to differ from those in the input. This can be done via the Advanced Settings:

  • Set a non-zero value for the target distance, typically 0.1 to 0.3 Angstrom. The target distance is the desired allowable change in heavy atom coordinates between the input and output structures.

  • Turn off the option to Restore Heavy Atom Coordinates.

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last update: Jan 28 2012