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 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:
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