TEST FILES FOR THP COORDINATES

This directory includes the file THP_FINAL_PDB.pdb that was generated from InsightII during regression testing of the phospho residue library scripts. The residue backbone atoms (HN-N-CA-C'-O) conformed to the AMBER and DYANA convention that require them to lie in a plane. These rotations were manually implemented in Insight II prior to exporting in the PDB formated file. This file was then reordered to follow additional conventions in the AMBER and DYANA libraries including minor updates to nomenclature. The resulting file in THP_FINAL_CHI.pdb. CHI is to indicate that the side chain chi angle are prescribe to 0 or 180 as is the convention in AMBER and DYANA.

pdb_renumber THP_FINAL_CHI.pdb > THP_FINAL_CHI_ORDER.pdb

The script pdb_renumber insures that the atom numbers are consecutive and increasing.

Matlab Processing

THP_FINAL_CHI_ORDER.pdb was then processed by the matlab scripts pdb2amber and pdb2dyana to build:

jwc_thp_regress_amber.pdb

jwc_thp_regress_dyana.pdb

Conversion to Internal Coordinates

Finally the publicly available file format convertor, babel, was used to specify the geometry in internal coordinates favored by many people.

babel jwc_thp_regress_amber.pdb -ofh jwc_thp_amber_internal.fh

babel jwc_thp_regress_dyana.pdb -ofh jwc_thp_dyana_internal.fh