X-PLOR Protein Structure Files (PSF)

Protein Structure Files (PSF) are used by EGO as a summary of the atom type, mass, partial charge and connectivity of the molecular system. PSF files are generated from the original PDB file in combination with X-PLOR topology file using X-PLOR.

The topology data files used by X-PLOR specify the atom parameters and connectivity for all amino acids and nucleotides. X-PLOR extracts all the information necessary (along with patches and modifications from the default configuration) for a given molecule in the PSF file in the form of:

1.

a list of atoms with the atom types (CH3E, CH1E, O, N, ...), partial charges and masses,

2.

a list of atom number pairs representing bonds,

3.

a list of atom number triples representing the angles between pairs of bonds,

4.

a list of atom number quadruples representing dihedral angles,

5.

atom number quadruples representing improper angles[3,4],

6.

atom numbers defining hydrogen bond donors and acceptors,

7.

explicit nonbonded interaction exclusions (See also Section 4.9).

An example PSF file follows (pti.psf):

PSF 
       4 !NTITLE
 REMARKS FILENAME="pti.psf"                                                     
 REMARKS BPTI COORDINATES TAKEN FROM CRISTALLOGRAPHIC DATA W/O WATERS           
 REMARKS HYDROGEN POSITIONS GENERATED USING HBUILD (2 ITERATIONS)               
 REMARKS RMS FLUCTUATIONS (T. ICHEYE) FOR HEAVY PROTEIN ATOMS INCLUDED          
 REMARKS DATE:24-Apr-89  02:34:58       created by user: heller                 

     568 !NATOM
       1 MAIN 1    ARG  HT1  HC     0.260000       1.00800           0
       2 MAIN 1    ARG  HT2  HC     0.260000       1.00800           0
       3 MAIN 1    ARG  N    NH3    0.000000E+00   14.0067           0
       4 MAIN 1    ARG  HT3  HC     0.260000       1.00800           0
...

     582 !NBOND: bonds
       3       5       5      18      18      19       5       6
       6       7       7       8       8       9       9      10
...

     834 !NTHETA: angles
       3       5      18       3       5       6       5      18      19
      18       5       6       5       6       7       6       7       8
...

     351 !NPHI: dihedrals
       3       5       6       7       5       6       7       8
       6       7       8       9       7       8       9      11
...

     259 !NIMPHI: impropers
       5       3      18       6       9       8      11      10
      11      12      15       9      22      20      25      23
...

     114 !NDON: donors
       9      10      12      13      12      14      15      16
      15      17       3       1       3       2       3       4
...

      79 !NACC: acceptors
      19      18      26      25      32      31      33      31
      35      34      47      46      54      53      63      62
...

      24 !NNB
      45      44      43      97      96      95     210     209
     208     224     223     222     236     235     234     328
...

     222       0 !NGRP
       0       0       0       5       0       0       7       0       0
...