APPENDIX D - PDB ATDL 1.1

The PDB ATDL (PDBA) File Format is another 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, REMARK records (one for each atom) were added at the beginning of file to store the non-standard data. The REMARK type is the user defined REMARK 78 (see PDB specifications). This rule was introduced to recognize custom records from standatd REMARKs. In each custom REMARK, some information are included as: atom number, atomic charge, atom type (that is force field-dependent) and ATDL atom description. This last item isn't fully exhaustive, because it ends at second level of the ATDL description.

         1         2         3         4
1234567890123456789012345678901234567890
REMARK  78 NNNNN CCC.CCCC FFFFFFFF ATDL

NNNNN   <- Atom number (C: %5d, Fortran: i5)
CC.CCCC <- Atom charge (C: %8.4f, Fortran: f8.4)
FFFF    <- Atom type (C: %-4.4s, Fortran: a4)
ATDL    <- ATDL description (free format, see ATDL specifications)

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

 

Example:
A3 molecule with TRIPOS atom types and Mopac atom charges.

REMARK   4
REMARK   4 File converted by VEGA V1.4.0
REMARK   4
REMARK  78     1  -0.1342 C.ar C-361 (C-361 C-361 H-100)
REMARK  78     2  -0.1211 C.ar C-361 (C-361 C-361 H-100)
REMARK  78     3   0.0103 C.ar C-361 (C-361 C-361 O-260)
REMARK  78     4   0.0127 C.ar C-361 (C-361 C-361 O-260)
REMARK  78     5  -0.1224 C.ar C-361 (C-361 C-361 H-100)
REMARK  78     6  -0.1317 C.ar C-361 (C-361 C-361 H-100)
REMARK  78     7   0.1346 H    H-100 (C-361)
REMARK  78     8   0.1490 H    H-100 (C-361)
REMARK  78     9   0.1495 H    H-100 (C-361)
REMARK  78    10   0.1351 H    H-100 (C-361)
REMARK  78    11  -0.2053 O.3  O-260 (C-361 C-460)
REMARK  78    12  -0.0061 C.3  C-460 (O-260 C-460 C-400 H-100)
REMARK  78    13  -0.0495 C.3  C-460 (C-460 O-260 H-100 H-100)
REMARK  78    14  -0.2028 O.3  O-260 (C-361 C-460)
REMARK  78    15   0.0983 H    H-100 (C-460)
REMARK  78    16   0.1358 H    H-100 (C-460)
REMARK  78    17  -0.0742 C.3  C-400 (C-460 N-300 H-100 H-100)
REMARK  78    18   0.1037 H    H-100 (C-460)
REMARK  78    19  -0.3024 N.3  N-300 (C-400 C-400 H-100)
REMARK  78    20   0.1057 H    H-100 (C-400)
REMARK  78    21   0.0759 H    H-100 (C-400)
REMARK  78    22  -0.0813 C.3  C-400 (N-300 C-400 H-100 H-100)
REMARK  78    23  -0.0242 C.3  C-400 (C-400 O-200 H-100 H-100)
REMARK  78    24   0.1049 H    H-100 (C-400)
REMARK  78    25   0.0725 H    H-100 (C-400)
REMARK  78    26  -0.1971 O.3  O-200 (C-400 C-361)
REMARK  78    27   0.0840 H    H-100 (C-400)
REMARK  78    28   0.0887 H    H-100 (C-400)
REMARK  78    29  -0.0066 C.ar C-361 (O-200 C-361 C-361)
REMARK  78    30   0.1008 C.ar C-361 (C-361 C-361 O-200)
REMARK  78    31  -0.2280 C.ar C-361 (C-361 C-361 H-100)
REMARK  78    32  -0.0676 C.ar C-361 (C-361 C-361 H-100)
REMARK  78    33  -0.2270 C.ar C-361 (C-361 C-361 H-100)
REMARK  78    34   0.0895 C.ar C-361 (C-361 C-361 O-200)
REMARK  78    35   0.1412 H    H-100 (C-361)
REMARK  78    36   0.1345 H    H-100 (C-361)
REMARK  78    37   0.1406 H    H-100 (C-361)
REMARK  78    38  -0.2037 O.3  O-200 (C-361 C-400)
REMARK  78    39  -0.0770 C.3  C-400 (O-200 H-100 H-100 H-100)
REMARK  78    40   0.1068 H    H-100 (C-400)
REMARK  78    41   0.0717 H    H-100 (C-400)
REMARK  78    42   0.0779 H    H-100 (C-400)
REMARK  78    43  -0.1905 O.3  O-200 (C-361 C-400)
REMARK  78    44  -0.0788 C.3  C-400 (O-200 H-100 H-100 H-100)
REMARK  78    45   0.1089 H    H-100 (C-400)
REMARK  78    46   0.0758 H    H-100 (C-400)
REMARK  78    47   0.0713 H    H-100 (C-400)
REMARK  78    48   0.1521 H    H-100 (N-300)
ATOM      1  C1  A3      1      -0.167   0.519  -0.316  1.00  0.00
ATOM      2  C2  A3      1       1.205   0.304  -0.310  1.00  0.00
ATOM      3  C3  A3      1       2.080   1.373  -0.177  1.00  0.00
ATOM      4  C4  A3      1       1.577   2.671  -0.061  1.00  0.00
ATOM      5  C5  A3      1       0.206   2.881  -0.062  1.00  0.00
ATOM      6  C6  A3      1      -0.667   1.809  -0.189  1.00  0.00
ATOM      7  H7  A3      1      -0.841  -0.318  -0.417  1.00  0.00
ATOM      8  H8  A3      1       1.601  -0.695  -0.405  1.00  0.00
ATOM      9  H9  A3      1      -0.173   3.887   0.035  1.00  0.00
ATOM     10  H10 A3      1      -1.733   1.980  -0.190  1.00  0.00
ATOM     11  O11 A3      1       3.444   1.107  -0.166  1.00  0.00
ATOM     12  C12 A3      1       4.203   2.182   0.346  1.00  0.00
ATOM     13  C13 A3      1       3.744   3.489  -0.311  1.00  0.00
ATOM     14  O14 A3      1       2.411   3.776   0.059  1.00  0.00
ATOM     15  H15 A3      1       3.813   3.412  -1.397  1.00  0.00
ATOM     16  H16 A3      1       4.382   4.319  -0.007  1.00  0.00
ATOM     17  C17 A3      1       5.678   1.886   0.076  1.00  0.00
ATOM     18  H18 A3      1       4.039   2.246   1.423  1.00  0.00
ATOM     19  N19 A3      1       6.547   2.933   0.612  1.00  0.00
ATOM     20  H20 A3      1       5.855   1.798  -0.997  1.00  0.00
ATOM     21  H21 A3      1       5.961   0.938   0.536  1.00  0.00
ATOM     22  C22 A3      1       7.967   2.742   0.320  1.00  0.00
ATOM     23  C23 A3      1       8.807   3.913   0.821  1.00  0.00
ATOM     24  H24 A3      1       8.092   2.633  -0.758  1.00  0.00
ATOM     25  H25 A3      1       8.294   1.815   0.791  1.00  0.00
ATOM     26  O26 A3      1      10.161   3.658   0.516  1.00  0.00
ATOM     27  H27 A3      1       8.681   4.035   1.898  1.00  0.00
ATOM     28  H28 A3      1       8.484   4.839   0.341  1.00  0.00
ATOM     29  C29 A3      1      10.955   4.719   0.921  1.00  0.00
ATOM     30  C30 A3      1      11.271   5.713   0.003  1.00  0.00
ATOM     31  C31 A3      1      12.069   6.782   0.410  1.00  0.00
ATOM     32  C32 A3      1      12.536   6.846   1.716  1.00  0.00
ATOM     33  C33 A3      1      12.215   5.847   2.625  1.00  0.00
ATOM     34  C34 A3      1      11.418   4.771   2.231  1.00  0.00
ATOM     35  H35 A3      1      12.341   7.576  -0.267  1.00  0.00
ATOM     36  H36 A3      1      13.151   7.677   2.027  1.00  0.00
ATOM     37  H37 A3      1      12.597   5.930   3.630  1.00  0.00
ATOM     38  O38 A3      1      11.039   3.720   3.067  1.00  0.00
ATOM     39  C39 A3      1      11.482   3.798   4.406  1.00  0.00
ATOM     40  H40 A3      1      11.115   2.931   4.956  1.00  0.00
ATOM     41  H41 A3      1      11.092   4.691   4.895  1.00  0.00
ATOM     42  H42 A3      1      12.572   3.787   4.458  1.00  0.00
ATOM     43  O43 A3      1      10.748   5.558  -1.281  1.00  0.00
ATOM     44  C44 A3      1      11.069   6.573  -2.210  1.00  0.00
ATOM     45  H45 A3      1      10.609   6.340  -3.170  1.00  0.00
ATOM     46  H46 A3      1      12.147   6.634  -2.365  1.00  0.00
ATOM     47  H47 A3      1      10.682   7.538  -1.882  1.00  0.00
ATOM     48  H48 A3      1       6.406   3.027   1.611  1.00  0.00
TER      49      A3      1
CONECT    1    2    6    7
CONECT    2    1    3    8
CONECT    3    2    4   11
CONECT    4    3    5   14
CONECT    5    4    6    9
CONECT    6    1    5   10
CONECT    7    1
CONECT    8    2
CONECT    9    5
CONECT   10    6
CONECT   11    3   12
CONECT   12   11   13   17   18
CONECT   13   12   14   15   16
CONECT   14    4   13
CONECT   15   13
CONECT   16   13
CONECT   17   12   19   20   21
CONECT   18   12
CONECT   19   17   22   48
CONECT   20   17
CONECT   21   17
CONECT   22   19   23   24   25
CONECT   23   22   26   27   28
CONECT   24   22
CONECT   25   22
CONECT   26   23   29
CONECT   27   23
CONECT   28   23
CONECT   29   26   30   34
CONECT   30   29   31   43
CONECT   31   30   32   35
CONECT   32   31   33   36
CONECT   33   32   34   37
CONECT   34   29   33   38
CONECT   35   31
CONECT   36   32
CONECT   37   33
CONECT   38   34   39
CONECT   39   38   40   41   42
CONECT   40   39
CONECT   41   39
CONECT   42   39
CONECT   43   30   44
CONECT   44   43   45   46   47
CONECT   45   44
CONECT   46   44
CONECT   47   44
CONECT   48   19
MASTER       51    0    0    0    0    0    0    0   48    1   48    0
END