Swart Lab - Theoretical Chemistry : pdb2adf/index.html

\(pdb2adf\)

program to prepare an ADF/AMS inputfile, starting from a PDB file
Current version: 2024.01 (shared with CC-BY-NC license). See also all python tools and software pages.

The \(pdb2adf\) program reads a PDB inputfile, recognizes the biochemical building blocks, and prepares an ADF inputfile from it. The program checks if atoms are missing, based on Amber template files, adds hydrogens automagically for the straightforward cases, and asks the user to choose between different options for the ambiguous cases.

References:

from PDB:

added hydrogens:

added waters:

Official PDB Format related to atomic coordinates:

  COLUMNS        DATA TYPE       FIELD         DEFINITION
--------------------------------------------------------------------------------
   1 -  6        Record name     "ATOM  "
   7 - 11        Integer         serial        Atom serial number.
  13 - 16        Atom            name          Atom name.
  17             Character       altLoc        Alternate location indicator.
  18 - 20        Residue name    resName       Residue name.
  22             Character       chainID       Chain identifier.
  23 - 26        Integer         resSeq        Residue sequence number.
  27             AChar           iCode         Code for insertion of residues.
  31 - 38        Real(8.3)       x             Orthogonal coordinates for X in
                                               Angstroms.
  39 - 46        Real(8.3)       y             Orthogonal coordinates for Y in
                                               Angstroms.
  47 - 54        Real(8.3)       z             Orthogonal coordinates for Z in
                                               Angstroms.
  55 - 60        Real(6.2)       occupancy     Occupancy.
  61 - 66        Real(6.2)       tempFactor    Temperature factor.
  73 - 76        LString(4)      segID         Segment identifier, left-justified.
  77 - 78        LString(2)      element       Element symbol, right-justified.
  79 - 80        LString(2)      charge        Charge on the atom.
--------------------------------------------------------------------------------

Examples
--------------------------------------------------------------------------------
ATOM     76  O   GLY    A9       6.671  55.354  35.873  1.00 14.75      A
ATOM     77  N   ASN   A10       6.876  53.257  36.629  1.00 16.09      A
--------------------------------------------------------------------------------
ATOM     20  P    DG A   2       8.226  23.537  13.511  1.00 32.21           P
ATOM     21  OP1  DG A   2       8.208  24.885  14.130  1.00 32.32           O
ATOM     22  OP2  DG A   2       7.338  23.230  12.365  1.00 32.24           O
ATOM     23  O5'  DG A   2       9.703  23.217  13.046  1.00 31.63           O
ATOM     24  C5'  DG A   2      10.746  23.398  13.956  1.00 31.13           C
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