APPENDIX D –  PDB Fat File Format 1.1

The PDB Fat (PDBF) File Format is a special version of the standard PDB. This format was created in order to include extra information keeping the compatibility with the Brookhaven National Library 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 function of the used force field) and the atomic partial charge:

         1         2         3         4
1234567890123456789012345678901234567890123
REMARK  77 EXTRA NNNNN EE FFFFFFFF  CC.CCCC

NNNNN    <- Atom number (C: %5d, Fortran: i5)
EE       <- Element (C: %-2.2s, Fortran: a2)
FFFFFFFF <- Atom type (C: %-8.8s, Fortran: a8)
CC.CCCC  <- Atom charge (C: %7.4f, Fortran: f7.4)

Warning:
Starting from 1.1 specifications, introduced with VEGA 1.5.0, the atom type format is changed in order to support the force fields with more than four character atom types (the limit is now eight characters).  The old 1.0 specifications are supported by VEGA in read mode for backward compatibility.

 

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
ATOM      1  C1  BEN     1       0.695   1.203   0.000  1.00  0.00
ATOM      2  C2  BEN     1      -0.695   1.203  -0.002  1.00  0.00
ATOM      3  C3  BEN     1      -1.389   0.000  -0.006  1.00  0.00
ATOM      4  C4  BEN     1      -0.695  -1.203  -0.007  1.00  0.00
ATOM      5  C5  BEN     1       0.695  -1.203  -0.006  1.00  0.00
ATOM      6  C6  BEN     1       1.389   0.000  -0.002  1.00  0.00
ATOM      7  H7  BEN     1       1.235   2.139   0.003  1.00  0.00
ATOM      8  H8  BEN     1      -1.235   2.139  -0.001  1.00  0.00
ATOM      9  H9  BEN     1      -2.470   0.000  -0.007  1.00  0.00
ATOM     10  H10 BEN     1      -1.235  -2.139  -0.010  1.00  0.00
ATOM     11  H11 BEN     1       1.235  -2.139  -0.007  1.00  0.00
ATOM     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