Example: pdb2adf transforms a PDB file to a QMMM input file
***********************************************************

"Download pdb2adf.run"

   #! /bin/sh

   # This example shows how to use the utility pdb2adf,
   # which creates an amsified ADF input file (ADF>=2020) from a PDB file,
   # for a subsequent QM/MM calculation using ADF.

   # -------------------------
   # First create the PDB file
   # -------------------------

   cat << eor > chymotrypsin.pdb
   HEADER    COMPLEX (SERINE PROTEASE/INHIBITOR)     12-MAR-97   1AFQ              
   TITLE     CRYSTAL STRUCTURE OF BOVINE GAMMA-CHYMOTRYPSIN COMPLEXED              
   TITLE    2 WITH A SYNTHETIC INHIBITOR                                           
   REMARK
   REMARK    Adaptation of original PDB file by M. Swart, March 2005
   REMARK    only coordinates of GAMMA-CHYMOTRYPSIN are kept;
   REMARK    rest has been deleted.
   REMARK
   ATOM      1  N   CYS A   1      13.717  20.021  22.754  1.00 13.46      PROA N  
   ATOM      2  CA  CYS A   1      14.211  18.932  23.617  1.00 13.34      PROA C  
   ATOM      3  C   CYS A   1      13.597  19.033  25.005  1.00 13.34      PROA C  
   ATOM      4  O   CYS A   1      12.953  20.026  25.329  1.00 13.48      PROA O  
   ATOM      5  CB  CYS A   1      15.734  19.018  23.753  1.00 13.44      PROA C  
   ATOM      6  SG  CYS A   1      16.298  20.647  24.361  1.00 13.30      PROA S  
   ATOM      7  N   GLY A   2      13.801  17.985  25.813  1.00 13.44      PROA N  
   ATOM      8  CA  GLY A   2      13.369  17.952  27.214  1.00 13.65      PROA C  
   ATOM      9  C   GLY A   2      11.904  18.088  27.631  1.00 13.87      PROA C  
   ATOM     10  O   GLY A   2      11.669  18.375  28.799  1.00 13.63      PROA O  
   ATOM     11  N   VAL A   3      10.947  17.887  26.732  1.00 14.18      PROA N  
   ATOM     12  CA  VAL A   3       9.559  17.968  27.090  1.00 14.86      PROA C  
   ATOM     13  C   VAL A   3       8.875  16.684  26.624  1.00 15.04      PROA C  
   ATOM     14  O   VAL A   3       8.529  16.546  25.452  1.00 14.91      PROA O  
   ATOM     15  CB  VAL A   3       8.861  19.211  26.437  1.00 15.00      PROA C  
   ATOM     16  CG1 VAL A   3       7.403  19.299  26.880  1.00 15.08      PROA C  
   ATOM     17  CG2 VAL A   3       9.585  20.486  26.805  1.00 15.27      PROA C  
   ATOM     18  N   PRO A   4       8.754  15.691  27.519  1.00 15.39      PROA N  
   ATOM     19  CA  PRO A   4       8.121  14.407  27.206  1.00 16.09      PROA C  
   ATOM     20  C   PRO A   4       6.675  14.535  26.769  1.00 16.35      PROA C  
   ATOM     21  O   PRO A   4       5.957  15.387  27.275  1.00 16.43      PROA O  
   ATOM     22  CB  PRO A   4       8.219  13.635  28.527  1.00 15.91      PROA C  
   ATOM     23  CG  PRO A   4       9.369  14.297  29.244  1.00 16.02      PROA C  
   ATOM     24  CD  PRO A   4       9.166  15.742  28.928  1.00 15.56      PROA C  
   ATOM     25  N   ALA A   5       6.262  13.690  25.827  1.00 16.87      PROA N  
   ATOM     26  CA  ALA A   5       4.874  13.703  25.351  1.00 17.53      PROA C  
   ATOM     27  C   ALA A   5       4.020  13.055  26.437  1.00 17.86      PROA C  
   ATOM     28  O   ALA A   5       2.862  13.413  26.643  1.00 17.81      PROA O  
   ATOM     29  CB  ALA A   5       4.740  12.936  24.027  1.00 17.34      PROA C  
   ATOM     30  N   ILE A   6       4.615  12.104  27.143  1.00 18.37      PROA N  
   ATOM     31  CA  ILE A   6       3.941  11.419  28.239  1.00 18.99      PROA C  
   ATOM     32  C   ILE A   6       4.553  11.993  29.514  1.00 19.59      PROA C  
   ATOM     33  O   ILE A   6       5.726  11.771  29.807  1.00 19.17      PROA O  
   ATOM     34  CB  ILE A   6       4.190   9.909  28.190  1.00 19.29      PROA C  
   ATOM     35  CG1 ILE A   6       3.631   9.335  26.886  1.00 19.66      PROA C  
   ATOM     36  CG2 ILE A   6       3.552   9.232  29.399  1.00 19.38      PROA C  
   ATOM     37  CD1 ILE A   6       3.977   7.887  26.674  1.00 20.59      PROA C  
   ATOM     38  N   GLN A   7       3.760  12.742  30.265  1.00 20.52      PROA N  
   ATOM     39  CA  GLN A   7       4.262  13.374  31.468  1.00 21.69      PROA C  
   ATOM     40  C   GLN A   7       4.683  12.459  32.597  1.00 22.02      PROA C  
   ATOM     41  O   GLN A   7       3.954  11.535  32.978  1.00 21.89      PROA O  
   ATOM     42  CB  GLN A   7       3.259  14.392  31.997  1.00 22.77      PROA C  
   ATOM     43  CG  GLN A   7       3.369  15.749  31.349  1.00 24.86      PROA C  
   ATOM     44  CD  GLN A   7       2.467  16.774  32.004  1.00 25.86      PROA C  
   ATOM     45  OE1 GLN A   7       1.660  17.417  31.337  1.00 27.24      PROA O  
   ATOM     46  NE2 GLN A   7       2.601  16.934  33.325  1.00 26.82      PROA N  
   ATOM     47  N   PRO A   8       5.898  12.675  33.125  1.00 22.41      PROA N  
   ATOM     48  CA  PRO A   8       6.345  11.830  34.231  1.00 22.84      PROA C  
   ATOM     49  C   PRO A   8       5.524  12.215  35.459  1.00 23.50      PROA C  
   ATOM     50  O   PRO A   8       5.069  13.359  35.575  1.00 23.62      PROA O  
   ATOM     51  CB  PRO A   8       7.821  12.219  34.389  1.00 22.58      PROA C  
   ATOM     52  CG  PRO A   8       7.864  13.641  33.894  1.00 22.61      PROA C  
   ATOM     53  CD  PRO A   8       6.972  13.583  32.678  1.00 22.34      PROA C  
   ATOM     54  N   VAL A   9       5.267  11.244  36.323  1.00 24.00      PROA N  
   ATOM     55  CA  VAL A   9       4.516  11.478  37.543  1.00 24.57      PROA C  
   ATOM     56  C   VAL A   9       5.471  11.122  38.665  1.00 24.99      PROA C  
   ATOM     57  O   VAL A   9       5.927   9.982  38.759  1.00 24.82      PROA O  
   ATOM     58  CB  VAL A   9       3.273  10.580  37.613  1.00 24.64      PROA C  
   ATOM     59  CG1 VAL A   9       2.596  10.725  38.969  1.00 24.88      PROA C  
   ATOM     60  CG2 VAL A   9       2.308  10.935  36.488  1.00 24.78      PROA C  
   ATOM     61  N   LEU A  10       5.827  12.119  39.464  1.00 25.78      PROA N  
   ATOM     62  CA  LEU A  10       6.752  11.921  40.568  1.00 26.56      PROA C  
   ATOM     63  C   LEU A  10       6.043  11.958  41.914  1.00 26.89      PROA C  
   ATOM     64  O   LEU A  10       5.187  12.847  42.105  1.00 27.07      PROA O  
   ATOM     65  CB  LEU A  10       7.857  12.973  40.501  1.00 26.93      PROA C  
   ATOM     66  CG  LEU A  10       8.721  12.752  39.255  1.00 27.39      PROA C  
   ATOM     67  CD1 LEU A  10       9.351  14.055  38.769  1.00 27.66      PROA C  
   ATOM     68  CD2 LEU A  10       9.768  11.681  39.555  1.00 27.46      PROA C  
   ATOM     69  OXT LEU A  10       6.329  11.066  42.743  1.00 27.55      PROA O  
   TER      70      LEU A  10                                                      
   END                                                                             
   eor

   # --------------------------------------------------------------------------------------
   # then run program to create ADF inputfile
   # The program works interactively. The input described here are answers to the questions
   # that were asked interactively.
   # In cases where the user agrees with the suggestion given by the program,
   # the user can press the **Enter** key, which is shown here with an empty line.
   # --------------------------------------------------------------------------------------

   $AMSBIN/pdb2adf << eor
   chymotrypsin.pdb




   3 4 5
   c
   5
   3 4 15 16
   c


   Y
   1
   1
   17.5
   eor

   # --------------------------------------------------------------------------------------
   # Questions asked were:
   #  Q1: Please give name of PDB-file
   #  A1: chymotrypsin.pdb
   #  Q2: Do you want a logfile to be written (Y/n) ?
   #  A2: Enter
   #  Q3: .. 
   #      Found the following terminal amino acid residues : (C-term)    10 (N-term)     1
   #      Do you want to use these as terminal residues (Y/n) ?
   #  A3: Enter
   #  Q4: Multiple AMBER options for CYS :
   #        0         Decide every time differently
   #        1   CYS   Cysteine (SH)                 
   #        2   CYM   Deprotonated Cysteine (S-)    
   #        3   CYX   Cystine (S-S bridge)          
   #      Suggested option: 0
   #  A4: Enter
   #  Q5: Multiple AMBER options for CYS    1 (    1) :
   #      ...
   #      Suggestion: 1
   #  A5: Enter
   #  Q6: ...
   #      Option  Molecule    Option  Molecule    Option  Molecule    Option  Molecule    Option  Molecule
   #           1: CYS    1         4: PRO    4         7: GLN    7        10: LEU   10
   #           2: GLY    2         5: ALA    5         8: PRO    8
   #           3: VAL    3         6: ILE    6         9: VAL    9
   #      Give option number of molecules to be put in QM region (or 'c' to continue):
   #      Note: by specifying a negative number a molecule is removed from the QM region
   #  A6: 3 4 5
   #  Q7:    ...
   #      Give option number of molecules to be put in QM region (or 'c' to continue):
   #      Note: by specifying a negative number a molecule is removed from the QM region
   #  A7: c
   #  Q8: Make a choice for the QM/MM treatment of VAL    3
   #       0:  Put completely in QM region
   #       1:  Cut off at C-alpha (put NH in QM region, CO in MM region)
   #       2:  Cut off at C-alpha (put NH in MM region, CO in QM region)
   #       3:  Cut off at C-alpha (put NH and CO in MM region)
   #       4:  Cut off at C-alpha (put NH and CO in QM region,  sidechain in MM region)
   #       5:  Put only part of sidechain in QM region
   #      Suggestion: 2
   #      Give choice:
   #  A8: 5
   #  Q9: Atoms belonging to molecule VAL     3
   #         1: N     MM                6: HB    MM               11: CG2   MM               16: O     MM
   #         2: H     MM                7: CG1   MM               12: HG21  MM
   #         3: CA    MM                8: HG11  MM               13: HG22  MM
   #         4: HA    MM                9: HG12  MM               14: HG23  MM
   #         5: CB    MM               10: HG13  MM               15: C     MM
   #      Give option number of atoms to be put in QM region (or 'c' to continue):
   #      (Note: a range can be entered as 3-21, while a negative number removes an atom)
   #  A9: 3 4 15 16
   # Q10: ...
   #      Give option number of atoms to be put in QM region (or 'c' to continue):
   #      (Note: a range can be entered as 3-21, while a negative number removes an atom)
   # A10: c
   # Q11: Make a choice for the QM/MM treatment of PRO    4
   #      ...
   #      Suggestion: 2
   # A11: Enter
   # Q12: Make a choice for the QM/MM treatment of ALA    5
   #      ...
   #      Suggestion: 1
   # A12: Enter
   # Q13: Do you want to add solvent to your system (Y/n) ?
   # A13: Y
   # Q14: Solvent (box) available:
   #         1:  HOH     HOH  Water molecule                     
   #         2:  MOH     MOH  Methanol molecule                  
   #         3:  CHL     CHL  Chloroform molecule
   # A14: 1
   # Q15: Box Shape options:
   #       1  Spherical box
   #       2  Cubic box
   # A15: 1
   # Q16: Give boxsize (def.:    16.71 Angs)
   # A16: 17.5
   # --------------------------------------------------------------------------------------

   # ----------------------------
   # now for checking correctness
   # ----------------------------

   echo ""
   echo "ADF inputfile made by pdb2adf"
   echo ""

   cat chymotrypsin.pdb2adf

   rm chymotrypsin.pdb chymotrypsin.pdb.log chymotrypsin.p2a.pdb chymotrypsin.pdb2adf
