APPENDIX D –  PDB Fat File Format 1.0.

The PDB Fat (PDBF) File Format is a special version of the standard PDB. This format was creared in order to include extra information keeping the compatibility with the Brookhaven National Laibrary specifications. For this reason, a sequence of REMARK records (one for each atom) was added at the beginning of file. The REMARK type is the user defined REMARK 77 (see PDB specifications) followed by the EXTRA keyword. This convention is needed to recognize the the special record from other REMARKs. The next record data are the atom number, the element, the atom type (in funcion of the used force field) and the atomic partial charge:

1234567890123456789012345678901234567890
REMARK  77 EXTRA NNNNN EE FFFF  CC.CCCC

NNNNN   <- Atom number (C: %5d, Fortran: i5)
EE      <- Element (C: %-2.2s, Fortran: a2)
FFFF    <- Atom type (C: %-4.4s, Fortran: a4)
CC.CCCC <- Atom charge (C: %7.4f, Fortran: f7.4)

 

Example:
a benzene with CVFF atom types and Gasteiger atom charges.

REMARK   4
REMARK   4 File converted by VEGA V1.1
REMARK   4
REMARK  77 EXTRA     1 C  cp    -0.0618
REMARK  77 EXTRA     2 C  cp    -0.0618
REMARK  77 EXTRA     3 C  cp    -0.0618
REMARK  77 EXTRA     4 C  cp    -0.0618
REMARK  77 EXTRA     5 C  cp    -0.0618
REMARK  77 EXTRA     6 C  cp    -0.0618
REMARK  77 EXTRA     7 H  h      0.0618
REMARK  77 EXTRA     8 H  h      0.0618
REMARK  77 EXTRA     9 H  h      0.0618
REMARK  77 EXTRA    10 H  h      0.0618
REMARK  77 EXTRA    11 H  h      0.0618
REMARK  77 EXTRA    12 H  h      0.0618
ATOMO     1  C1  BEN     1       0.695   1.203   0.000  1.00  0.00
ATOMO     2  C2  BEN     1      -0.695   1.203  -0.002  1.00  0.00
ATOMO     3  C3  BEN     1      -1.389   0.000  -0.006  1.00  0.00
ATOMO     4  C4  BEN     1      -0.695  -1.203  -0.007  1.00  0.00
ATOMO     5  C5  BEN     1       0.695  -1.203  -0.006  1.00  0.00
ATOMO     6  C6  BEN     1       1.389   0.000  -0.002  1.00  0.00
ATOMO     7  H7  BEN     1       1.235   2.139   0.003  1.00  0.00
ATOMO     8  H8  BEN     1      -1.235   2.139  -0.001  1.00  0.00
ATOMO     9  H9  BEN     1      -2.470   0.000  -0.007  1.00  0.00
ATOMO    10  H10 BEN     1      -1.235  -2.139  -0.010  1.00  0.00
ATOMO    11  H11 BEN     1       1.235  -2.139  -0.007  1.00  0.00
ATOMO    12  H12 BEN     1       2.470   0.000  -0.001  1.00  0.00
TER      13      BEN     1
CONECT    1    2    6    7
CONECT    2    1    3    8
CONECT    3    2    4    9
CONECT    4    3    5   10
CONECT    5    4    6   11
CONECT    6    1    5   12
CONECT    7    1
CONECT    8    2
CONECT    9    3
CONECT   10    4
CONECT   11    5
CONECT   12    6
MASTER       15    0    0    0    0    0    0    0   12    1   12    0
END