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 (9th column) and harmonic force (10th 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/ . 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.