Brookhaven PDB Atom Coordinate Files

The Brookhaven PDB file format can contain various information to describe molecular systems, but EGO uses only ATOM records to identify atom coordinates and stochastic boundary parameters (when used on a per atom basis, see Section 4.19) and Section 4.20. For a given atom, the atom type, mass and partial charge information is provided in the corresponding PSF file generated by X-PLOR from the PDB file and topology files.

ATOM records appear in the PDB file as follows (as an example we show parts of the file pti.pdb):

REMARK FILENAME="pti.pdb"
REMARK BPTI COORDINATES TAKEN FROM CRISTALLOGRAPHIC DATA W/O WATERS
REMARK HYDROGEN POSITIONS GENERATED USING HBUILD (2 ITERATIONS)
REMARK RMS FLUCTUATIONS (T. ICHEYE) FOR HEAVY PROTEIN ATOMS INCLUDED
REMARK DATE:24-Apr-89  02:35:12       created by user: heller
ATOM      1  HT1 ARG     1      27.077  26.629  -3.076  1.00  0.00      MAIN
ATOM      2  HT2 ARG     1      27.163  28.116  -2.262  1.00  0.00      MAIN
ATOM      3  N   ARG     1      26.522  27.417  -2.687  1.00  0.57      MAIN
...
ATOM    567  OT1 ALA    58      26.421  31.411  -8.486  1.00  0.74      MAIN
ATOM    568  OT2 ALA    58      25.216  33.274  -8.900  1.00  0.78      MAIN
END

The REMARK lines are comments which are ignored by EGO. The ATOM record consists of atom number, atom name, residue name, residue number, the x, y, z coordinates of the atom in Å, followed by friction parameter (9^th column) and harmonic force (10^th column) constant. The friction parameter is only used in case that the stochastic boundary is enabled in the control file ctl.lis, and atoms with non-zero harmonic force constants are bound to their reference position, taken from coord.lis, with the harmonic force constant. Units are generally given in terms of Å for distance, and kcal/mol for energy, therefore, a harmonic force constant, k, is given in units of kcal/mol/ ${\rm\AA}^2$. The friction constant is given in ps^-1. Included in the EGO distribution is the X-PLOR-script $(HOME)/ego/utils/boundary.inp, which demonstrates how to set up harmonic restraints and friction factors for a selection of atoms.