pdb2adf: transform PDB file to QMMM input file

The pdb2adf utility program was written by Marcel Swart.

Overview

General description

Starting from the ADF2005.01 version the utility pdb2adf is available in the official release. Previously this utility could be found on the contributed software page. Starting from AMS2020 the default is to make an amsified ADF input, which can not be used with previous versions. One can get the old style input if the environment variable SCM_PDB2ADF is set to OLD (only to be used with ADF<=2019). One can get the NEWQMMM style input input if the environment variable SCM_PDB2ADF is set to NEW (only to be used with ADF<=2019).

The pdb2adf utility was written to read a PDB file, which contains the atomic coordinates of a protein structure, and transform it into an ADF inputfile, particularly for use with QMMM calculations. It can also be used for setting up a solvent shell around a solute molecule.

The PDB files are generally used for protein structures, and are formatted according to certain rules, see: http://www.wwpdb.org/docs.html, and the part about the official PDB format below.

For every residue/molecule present in the PDB file, there should be a fragment file available, either in the general AMS library ($AMSHOME/atomicdata/pdb2adf directory), or in the local directory where the pdb2adf program is being called. Fragment files in the local directory take higher priority than those in the general AMS library. The fragment files are formatted, based loosely on AMBER parameter files, and contain information about the residues; e.g., the atoms present, with their general and forcefield atomnames, atomic charges, connections to other atoms for creating their positions when not found on the PDB file, etc.; see part about fragment files below. Available in the AMS library are fragment files for amino acid residues, including those at the N- or C-terminal residue, three solvents (water, methanol, chloroform), some ions that are present frequently in protein structures (copper, fluoride), etc.

Also present in the AMS library are solvent box files that can be used to place a layer of solvents surrounding the protein, or a solute. Available are the three solvents mentioned above.

After reading the PDB and corresponding fragment files, the program tries to figure out which atoms are missing, and will add those; it uses the information provided on the fragment files to do so. For certain amino acid residues, there are several protonation states possible, e.g. histidine can be protonated at the N-delta position, at the N-epsilon position, or on both. The default option is to choose the fully charged option for aspartate (Asp), glutamate (Glu), lysine (Lys) residues, and decide for each histidine (His) and cysteine (Cys) residue individually what the protonation state should be. In those individual cases, the distances of neighboring molecules/residues are given that may help determine the protonation state. See the protein example below.

After all that is setup properly, a list is given with residue names/numbers, from which you can choose those that should be placed in the QM system; afterwards, for each of the selected QM residues, a choice should be made where to cut-off the QM part. The most appropriate point to cut-off seems to be at the C-alpha position, except when dealing with a proline (Pro). The latter residue is cyclic, e.g. the sidechain is connected to the C-alpha carbon ! For that residue, it may be better to include the C-alpha, H-alpha, and backbone carbonyl group of the preceding residue in the QM part.

The program will try to use to replace the “.pdb” extension of the PDB file by “.pdb2adf” for the AMS inputfile to be made; for convenience, the program also writes out an “.p2a.pdb” file with the complete system as it being made by the program. This file can then be visualized by conventional viewer programs (such as iMol, VMD, Molekel, AMSview) for visual inspection if everything has been carried out correctly.

Given below are two examples, one for the application of a protein, the other how to set up a solvent shell run.

Things to notice

  • The QMMM implementation in AMS2020 is new. It uses the AMS Hybrid engine.

  • By default pdb2adf makes an AMS Hybrid Engine input format.

  • The pdb2adf program uses AMBER parameter files, and is setup to work with the AMBER force field, version AMBER95, which is designed for and works well for biosystems.

  • For questions, remarks, contact: support@scm.com.

For ADF<=2019 only:

  • The old style QMMM input format is used if the environment variable SCM_PDB2ADF is set to OLD.

  • The NEWQMMM style QMMM input format is used if the environment variable SCM_PDB2ADF is set to NEW.

Official PDB format

Columns

Data Type

Field

Definition

1 - 6

Record name

‘ATOM’ or ‘HETATM’

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

borderleft 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.

Typical examples from PDB-files:

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890

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     62  O   GLY A   9       6.791  55.214  35.719  1.00 15.61      4AZU 153
ATOM     63  N   ASN A  10       6.892  53.135  36.555  1.00 12.64      4AZU 154

The pdb2adf utility is flexible, and should be able to read most PDB files, even those with incomplete or erroneous line formats. From every ATOM/HETATM line, it tries to read:

  • atom number

  • atom name

  • residuename

  • chain identifier

  • residue number

  • X,Y,Z coordinates

Hints for proper formatting:

  • always group together atoms that belong to one residue

  • always give the atom name on columns 13-16

  • when specifying a chain-id use only letters (or a blank)

Contents of fragment file

Given below is the contents of the fragment file for water. The first line is a comment line, the only important parameter is the NOCONNECT keyword, which indicates that the program should not try to make any connections to other residues/molecules. Then follow three lines, that define the orientation in space of the residue; they are not used for general fragments, but are relevant and important for amino acid residues and DNA nucleotides. Finally, for each atom in the molecule, there should be a line with its number in the fragment; its name to be used in PDB files; the AMBER forcefield atomtype; a dummy atomname; connections and coordinates (bond, angle, dihedral angle) to other atoms in the molecule that can be used to give the position of the atom if it is not present in the PDB file; the atomic charge; and after the exclamation mark (!) the connections to other atoms in this fragment, or other fragments in case of amino acid residues/DNA nucleotides. The current version does not use the latter connections yet, but the next version will probably use them.

HOH  Water molecule  NOCONNECT
   1   DUMM  DU    M      0   0   0       0.0000      0.0000      0.0000
   2   DUMM  DU    M      1   0   0       1.4490      0.0000      0.0000
   3   DUMM  DU    M      2   1   0       1.5220    111.1000      0.0000
   4   O     OW    O      0   0   0       0.0000      0.0000      0.0000  -0.8340  !  5  6
   5   H1    HW    H      4   0   0       0.9572      0.0000      0.0000   0.4170  !  4
   6   H2    HW    H      4   5   0       0.9572    104.5200      0.0000   0.4170  !  4

Contents of solvent box files

The first line is a comment line, followed by a line with the total number of atoms in the solvent box and the dimensions of the box (in Angstroms); then for each atom in the box, the atom name, which must match the PDB atomname, and the Cartesian coordinates, again in Angstroms.

Usage of pdb2adf

Short description

The program works interactively, and should be straightforwardly to use. However, for some of the stages in the output a short description is given below.

                                  P D B 2 A D F - program
                                     version 2008.01
                              Written by: Marcel Swart, 2008

                         This program uses AMBER parameter files
                            see: http://amber.scripps.edu

Do you want a logfile to be written (Y/n) ?

This option exists to create a logfile of what pdb2adf does. However, it should normally be used only for debugging purposes.

Ignoring atom on line:
ATOM    974   OH LYS A 128     -10.073 42.775 15.690 1.00 38.79     5AZU1065

This is a warning that the atom on that particular line is ignored, should normally occur only few times (less than ten). Depends also on how well the PDB file follows the PDB format rules.

Data Processed:
     Nat:       2519
    Nmol:        196
 NChains:          1

Information about what has been read on the PDB file: the total number of atoms (Nat), number of molecules/residues (Nmol) and number of protein chains (Nchains).

Please wait, making connection tables

At this point, the connections between the atoms are being made by looking at atom distances. It may take a while, depending on the size of the system.

Do you want to make separate files for each chain (Y/n) ?

You have the option to make different inputfiles for different protein chains, but you can also make one inputfile for all of them together.

Found the following terminal amino acid residues : (C-term) 128 (N-term) 1
Do you want to use these as terminal residues (Y/n) ?

Info is given about the C- and N-terminal residue of each chain. Reported for making sure they are chosen correctly. Note, if the C- and N-terminal residues are connected (rarely the case probably), enter N here.

Multiple AMBER options for HIS :
  0         Decide every time differently
  1   HID   Histidine Delta Hydrogen
  2   HIE   Histidine Epsilon Hydrogen
  3   HIP   Histidine E & D Hydrogens

Suggested option: 0

For a number of residues (His, Glu, Asp, Lys and Cys) there is more than one option available in the AMBER95 force field, depending on the protonation state (His, Glu, Asp and Lys) or the existence of a sulphur bridge/connection to a metal atom (Cys). The default is to choose a different option for the His and Cys residues, and use one option for Glu, Asp and Lys (fully charged). However, if wanted you can make a choice for all residues.

Multiple AMBER options for CYS    3 (    3) :
  1   CYS   Cysteine (SH)
  2   CYM   Deprotonated Cysteine (S-)
  3   CYX   Cystine (S-S bridge)

  Connections and Nearest Atoms for SG CYS    3 SG  ( P2A #   41 PDB#   20 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.82      38      19  CB  CYS    3  CB       1       3.79    2382     980  O   HOH  151  O
 2    2.02     461     193  SG  CYS   26  SG       2       3.80      22       0  HC  GLN    2
                                                   3       4.04    2391     983  O   HOH  154  O
                                                   4       4.15     509     206  O   GLN   28  O
                                                   5       4.18     522       0  HA  PHE   29
Suggestion: 3

The options for Cys3 are given, with information about the atoms bonded to the SG sulphur atom (on the left), as well as the closest five non-bonded atoms (on the right). This information may help you decide which choice to make for this particular residue. Also given (on the bottom) is the suggested choice, which is based, in this case, on the presence of a sulphur bridge.

Multiple AMBER options for HIS   46 (   46) :
  1   HID   Histidine Delta Hydrogen
  2   HIE   Histidine Epsilon Hydrogen
  3   HIP   Histidine E & D Hydrogens

  Connections and Nearest Atoms for ND HIS   46 ND1 ( P2A #  844 PDB#  347 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.37     843     346  CG  HIS   46  CG       1       2.62    2166       0  H1  MET  121
 2    1.33     846     349  CE  HIS   46  CE1      2       3.23    2080     863  ND  HIS  117  ND1
 3    2.04    2318     959  CU  CU   130  CU       3 HB    3.33    2163     900  S   MET  121  SD
                                                   4       3.40    2164     901  CT  MET  121  CE
                                                   5       3.57    2082     865  CE  HIS  117  CE1

  Connections and Nearest Atoms for NE HIS   46 NE2 ( P2A #  848 PDB#  350 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.32     846     349  CE  HIS   46  CE1      1 HB    2.70     162      67  O   ASN   10  O
 2    1.37     850     348  CD  HIS   46  CD2      2       2.83     814       0  H1  MET   44
                                                   3       3.23    2166       0  H1  MET  121
                                                   4       3.52     822     332  O   MET   44  O
                                                   5       3.74     813     334  CT  MET   44  CG
Suggestion: 2

For His residues, the information is given for both the delta- and the epsilon nitrogen atoms. Also indicated (by HB) is the presence of a hydrogen bond with another atom. The definition used here is that two atoms are hydrogen bonded if they are both non-carbon/non-hydrogen atoms, and the distance between them is less than the sum of the van der Waals radii of the atoms. It is a simple definition, but seems to be effective. In this case, as the N(delta) is bonded to copper, the proton should be attached to the N(epsilon).

Making choice for which molecules should be QM, which MM

Now we come to the part where the division in the QM and MM systems is made.

Residues belonging to chain  0
Option  Molecule    Option  Molecule    Option  Molecule    Option  Molecule    Option  Molecule
     1: ALA    1        28: GLN   28        55: ASP   55        82: ALA   82       109: ALA  109
     2: GLN    2        29: PHE   29        56: LYS   56        83: HIS   83       110: TYR  110
etc

All molecules/residues belonging to chain 0 are given, with an option number.

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

Here you are asked to enter the option numbers of the residues you want to put in the QM system.

Putting GLY   45 in QM region
Putting HIS   46 in QM region

In this case, Gly45 and His46 have been put in the QM system.

Make a choice for the QM/MM treatment of GLY   45
 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:

A choice should be made for where to cut-off the QM system. Normally this is done at the C(alpha) position, and you should simply choose the Suggestion.

Solvent molecules (SOL/HOH) belonging to this chain:
    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20
   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40
   41   42   43   44   45   46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
   61   62   63   64   65   66

Give the number of the molecule to be put in QM region (or 'c' to continue):

Also water molecules can be put in the QM system.

Box Shape options:
 1  Spherical box
 2  Cubic box
Make a choice:

Type of box to be used.

Maximum atomic distance (Angs) from center       25.62
Give boxsize (def.:    28.62 Angs)

Size of box to be used to put a layer of solvent molecules around the system. Max. dist. is the maximal distance of any protein atom from the center of mass of the protein. Usually you should choose a boxsize at least 6 Angstrom larger (so at least two solvent molecules are surrounding the system).

Using BOXSIZE value of  30.0000
Adding atoms for box     1  Added (Box):     0 (Total):     0  Excl. (1):   648  Excl. (2):     0
Adding atoms for box     2  Added (Box):     9 (Total):     9  Excl. (1):   639  Excl. (2):     0
Adding atoms for box    63  Added (Box):     3 (Total):  7635  Excl. (1):   645  Excl. (2):     0
Adding atoms for box    64  Added (Box):     0 (Total):  7635  Excl. (1):   648  Excl. (2):     0
Writing inputfile for chain   1

A total amount of 7635 atoms (2545 water molecules) has been added.

Inputfile(s) written, everything processed, work has been done.
Thank you for using the PDB2ADF program.

================================
Normal ending of PDB2ADF program
================================

ADF inputfile(s) have been written, the PDB-file has been processes. Everything is done.

An example on protein structure

The idea of this example is to make an adf-input file using a PDB of an azurin (1DYZ.pdb.txt). The result of this example should be that in the adf-input file the active site of azurin (Figure 1) is in the QM part, and the rest of the protein is in the MM part, and that the solvent water is added (in a box), which is also in the MM part.

/scm-uploads/doc.trunk/Hybrid/_images/azurin.png

Figure 1: the active site of azurin

Usage of pdb2adf

The program works interactively. Given below in bold are the parts that the user has to type. In cases where the user agrees with the suggestion given by the program, the user can press the Enter key indicated with Enter.

                                  P D B 2 A D F - program
                                     version 2008.01
                              Written by: Marcel Swart, 2008

                         This program uses AMBER parameter files
                            see: http://amber.scripps.edu

Please give name of PDB-file

1DYZ.pdb.txt

Do you want a logfile to be written (Y/n) ?

Enter

 read fragments

Data Processed:
     Nat:       2519
    Nmol:        196
 NChains:          1

Please wait, making connection tables
Now finding nearby atoms
Assigning chain ID to all residues
Completing residues for which only option is available

Found the following terminal amino acid residues : (C-term)   129 (N-term)     1
Do you want to use these as terminal residues (Y/n) ?

Enter

Refinding nearby atoms (including atoms added in residue completion)

Multiple AMBER options for HIS :
  0         Decide every time differently
  1   HID   Histidine Delta Hydrogen
  2   HIE   Histidine Epsilon Hydrogen
  3   HIP   Histidine E & D Hydrogens

Suggested option: 0

Enter

Using 0: Decide every time differently

Multiple AMBER options for GLU :
  0         Decide every time differently
  1   GLU   Glutamic acid (COO-)
  2   GLH   Neutral Glutamic acid (COOH)

Suggested option: 1

Enter

Using 17   GLU   Glutamic acid (COO-)

Multiple AMBER options for ASP :
  0         Decide every time differently
  1   ASP   Aspartic acid (COO-)
  2   ASH   Neutral Aspartatic acid (COOH)

Suggested option: 1

Enter

Using 18   ASP   Aspartic acid (COO-)

Multiple AMBER options for LYS :
  0         Decide every time differently
  1   LYS   Charged Lysine (NH3+)
  2   LYN   Neutral Lysine (NH2)

Suggested option: 1

Enter

Using 19   LYS   Charged Lysine (NH3+)

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

Enter

Using 0: Decide every time differently
 - - - - - - - - - - - - - - - - - - - - - - - - - - -
           Making Choices for Chain      0
 - - - - - - - - - - - - - - - - - - - - - - - - - - -

Multiple AMBER options for CYS    3 (    3) :
  1   CYS   Cysteine (SH)
  2   CYM   Deprotonated Cysteine (S-)
  3   CYX   Cystine (S-S bridge)

  Connections and Nearest Atoms for SG CYS    3 SG  ( P2A #   41 PDB#   20 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.82      38      19  CB  CYS    3  CB       1       3.79    2382     980  O   HOH  151  O
 2    2.02     461     193  SG  CYS   26  SG       2       3.80      22       0  HC  GLN    2
                                                   3       4.04    2391     983  O   HOH  154  O
                                                   4       4.15     509     206  O   GLN   28  O
                                                   5       4.18     522       0  HA  PHE   29
Suggestion: 3

Enter

Multiple AMBER options for CYS   26 (   26) :
  1   CYS   Cysteine (SH)
  2   CYM   Deprotonated Cysteine (S-)
  3   CYX   Cystine (S-S bridge)

  Connections and Nearest Atoms for SG CYS   26 SG  ( P2A #  461 PDB#  193 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.82     458     192  CB  CYS   26  CB       1       3.41     522       0  HA  PHE   29
 2    2.02      41      20  SG  CYS    3  SG       2       3.43     411     168  O   ASP   23  O
                                                   3       3.60    2322     960  O   HOH  131  O
                                                   4       3.91     403     169  CB  ASP   23  CB
                                                   5       4.15     387       0  HC  VAL   22
Suggestion: 3

Enter

Multiple AMBER options for HIS   32 (   32) :
  1   HID   Histidine Delta Hydrogen
  2   HIE   Histidine Epsilon Hydrogen
  3   HIP   Histidine E & D Hydrogens

  Connections and Nearest Atoms for ND HIS   32 ND1 ( P2A #  581 PDB#  244 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.39     580     243  CG  HIS   32  CG       1       3.41     545       0  HC  THR   30
 2    1.33     583     246  CE  HIS   32  CE1      2       3.43      76      33  O   ALA    5  O
                                                   3       3.58      90      40  OH  THR    6  OG1
                                                   4       3.99      91       0  HO  THR    6
                                                   5       4.17      68       0  H   ALA    5

  Connections and Nearest Atoms for NE HIS   32 NE2 ( P2A #  585 PDB#  247 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.31     583     246  CE  HIS   32  CE1      1       2.86     544       0  HC  THR   30
 2    1.37     587     245  CD  HIS   32  CD2      2       3.00     545       0  HC  THR   30
                                                   3       3.14    1677       0  HO  SER   94
                                                   4       3.42     542     229  CT  THR   30  CG2
                                                   5       3.65    1676     688  OH  SER   94  OG
Suggestion: 1

3

Multiple AMBER options for HIS   35 (   35) :
  1   HID   Histidine Delta Hydrogen
  2   HIE   Histidine Epsilon Hydrogen
  3   HIP   Histidine E & D Hydrogens

  Connections and Nearest Atoms for ND HIS   35 ND1 ( P2A #  649 PDB#  271 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.38     648     270  CG  HIS   35  CG       1       2.46     682       0  H   GLY   37
 2    1.32     651     273  CE  HIS   35  CE1      2       2.69    1604       0  H1  GLY   89
                                                   3       3.31     681     282  N   GLY   37  N
                                                   4       3.56    1602     653  CT  GLY   89  CA
                                                   5       3.67     152       0  H1  ASN   10

  Connections and Nearest Atoms for NE HIS   35 NE2 ( P2A #  653 PDB#  274 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.33     651     273  CE  HIS   35  CE1      1 HB    2.91     822     332  O   MET   44  O
 2    1.37     655     272  CD  HIS   35  CD2      2       3.24     814       0  H1  MET   44
                                                   3       3.24     850     348  CD  HIS   46  CD2
                                                   4       3.34    1593       0  H1  GLY   88
                                                   5       3.75     848     350  NE  HIS   46  NE2
Suggestion: 2

3

Multiple AMBER options for HIS   46 (   46) :
  1   HID   Histidine Delta Hydrogen
  2   HIE   Histidine Epsilon Hydrogen
  3   HIP   Histidine E & D Hydrogens

  Connections and Nearest Atoms for ND HIS   46 ND1 ( P2A #  844 PDB#  347 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.37     843     346  CG  HIS   46  CG       1       2.62    2166       0  H1  MET  121
 2    1.33     846     349  CE  HIS   46  CE1      2       3.23    2080     863  ND  HIS  117  ND1
 3    2.04    2318     959  CU  CU   130  CU       3 HB    3.33    2163     900  S   MET  121  SD
                                                   4       3.40    2164     901  CT  MET  121  CE
                                                   5       3.57    2082     865  CE  HIS  117  CE1

  Connections and Nearest Atoms for NE HIS   46 NE2 ( P2A #  848 PDB#  350 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.32     846     349  CE  HIS   46  CE1      1 HB    2.70     162      67  O   ASN   10  O
 2    1.37     850     348  CD  HIS   46  CD2      2       2.83     814       0  H1  MET   44
                                                   3       3.23    2166       0  H1  MET  121
                                                   4       3.52     822     332  O   MET   44  O
                                                   5       3.74     813     334  CT  MET   44  CG
Suggestion: 2

Enter

Multiple AMBER options for HIS   83 (   83) :
  1   HID   Histidine Delta Hydrogen
  2   HIE   Histidine Epsilon Hydrogen
  3   HIP   Histidine E & D Hydrogens

  Connections and Nearest Atoms for ND HIS   83 ND1 ( P2A # 1494 PDB#  613 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.39    1493     612  CG  HIS   83  CG       1       2.67    1317       0  HC  VAL   73
 2    1.33    1496     615  CE  HIS   83  CE1      2       3.63    1315     542  CT  VAL   73  CG2
                                                   3       3.74    1310       0  HC  VAL   73
                                                   4       3.82    1316       0  HC  VAL   73
                                                   5       3.86    1313       0  HC  VAL   73

  Connections and Nearest Atoms for NE HIS   83 NE2 ( P2A # 1498 PDB#  616 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.32    1496     615  CE  HIS   83  CE1      1       3.09    1313       0  HC  VAL   73
 2    1.38    1500     614  CD  HIS   83  CD2      2       3.44    1317       0  HC  VAL   73
                                                   3       3.88    2385     981  O   HOH  152  O
                                                   4       3.93    1311     541  CT  VAL   73  CG1
                                                   5       4.03    1309     540  CT  VAL   73  CB
Suggestion: 2

3

Multiple AMBER options for CYS  112 (  112) :
  1   CYS   Cysteine (SH)
  2   CYM   Deprotonated Cysteine (S-)
  3   CYX   Cystine (S-S bridge)

  Connections and Nearest Atoms for SG CYS  112 SG  ( P2A # 2001 PDB#  828 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.82    1998     827  CB  CYS  112  CB       1       2.53     858       0  H   ASN   47
 2    2.14    2318     959  CU  CU   130  CU       2       2.65    2023       0  H   PHE  114
                                                   3       3.00    2028       0  HC  PHE  114
                                                   4       3.29     868       0  H   ASN   47
                                                   5       3.39    2027       0  HC  PHE  114
Suggestion: 2

Enter

Multiple AMBER options for HIS  117 (  117) :
  1   HID   Histidine Delta Hydrogen
  2   HIE   Histidine Epsilon Hydrogen
  3   HIP   Histidine E & D Hydrogens

  Connections and Nearest Atoms for ND HIS  117 ND1 ( P2A # 2080 PDB#  863 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.37    2079     862  CG  HIS  117  CG       1       2.82    2028       0  HC  PHE  114
 2    1.34    2082     865  CE  HIS  117  CE1      2       3.23     844     347  ND  HIS   46  ND1
 3    1.99    2318     959  CU  CU   130  CU       3       3.26    2031       0  HA  PHE  114
                                                   4       3.27     832     340  O   GLY   45  O
                                                   5       3.43     846     349  CE  HIS   46  CE1

  Connections and Nearest Atoms for NE HIS  117 NE2 ( P2A # 2084 PDB#  866 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.31    2082     865  CE  HIS  117  CE1      1       2.57     209       0  H1  MET   13
 2    1.37    2086     864  CD  HIS  117  CD2      2       2.65    2031       0  HA  PHE  114
                                                   3 HB    2.74    2406     988  O   HOH  159  O
                                                   4       3.34    2030     841  CA  PHE  114  CD1
                                                   5       3.41     204       0  H1  MET   13
Suggestion: 2

Enter

 - - - - - - - - - - - - - - - - - - - - - - - - - - -
           Making Choices for Chain      1
 - - - - - - - - - - - - - - - - - - - - - - - - - - -

Completing residues with multiple options available, and solvent molecules

Checking positions of newly added atoms

Making choice for which molecules should be QM, which MM

Residues belonging to chain  0
Option  Molecule    Option  Molecule    Option  Molecule    Option  Molecule    Option  Molecule
     1: ALA    1        28: GLN   28        55: ASP   55        82: ALA   82       109: ALA  109
     2: GLN    2        29: PHE   29        56: LYS   56        83: HIS   83       110: TYR  110
     3: CYS    3        30: THR   30        57: GLN   57        84: THR   84       111: PHE  111
     4: GLU    4        31: MET   31        58: ALA   58        85: LYS   85       112: CYS  112
     5: ALA    5        32: HIS   32        59: VAL   59        86: VAL   86       113: SER  113
     6: THR    6        33: LEU   33        60: ALA   60        87: ILE   87       114: PHE  114
     7: VAL    7        34: LYS   34        61: THR   61        88: GLY   88       115: PRO  115
     8: GLU    8        35: HIS   35        62: ASP   62        89: GLY   89       116: GLY  116
     9: SER    9        36: VAL   36        63: GLY   63        90: GLY   90       117: HIS  117
    10: ASN   10        37: GLY   37        64: MET   64        91: GLU   91       118: TRP  118
    11: ASP   11        38: LYS   38        65: GLY   65        92: SER   92       119: ALA  119
    12: ALA   12        39: MET   39        66: ALA   66        93: ASP   93       120: MET  120
    13: MET   13        40: ALA   40        67: GLY   67        94: SER   94       121: MET  121
    14: GLN   14        41: LYS   41        68: LEU   68        95: VAL   95       122: LYS  122
    15: TYR   15        42: VAL   42        69: ALA   69        96: THR   96       123: GLY  123
    16: ASN   16        43: ALA   43        70: GLN   70        97: PHE   97       124: THR  124
    17: VAL   17        44: MET   44        71: ASP   71        98: ASP   98       125: LEU  125
    18: LYS   18        45: GLY   45        72: TYR   72        99: VAL   99       126: LYS  126
    19: GLU   19        46: HIS   46        73: VAL   73       100: SER  100       127: LEU  127
    20: ILE   20        47: ASN   47        74: LYS   74       101: LYS  101       128: GLY  128
    21: VAL   21        48: LEU   48        75: ALA   75       102: ILE  102       129: SER  129
    22: VAL   22        49: VAL   49        76: GLY   76       103: ALA  103       130: CU   130
    23: ASP   23        50: LEU   50        77: ASP   77       104: ALA  104
    24: LYS   24        51: THR   51        78: THR   78       105: GLY  105
    25: SER   25        52: LYS   52        79: ARG   79       106: GLU  106
    26: CYS   26        53: ASP   53        80: VAL   80       107: ASN  107
    27: LYS   27        54: ALA   54        81: ILE   81       108: TYR  108

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

45 46 112 117 121 130

Putting GLY   45 in QM region
Putting HIS   46 in QM region
Putting CYS  112 in QM region
Putting HIS  117 in QM region
Putting MET  121 in QM region
Putting CU   130 in QM region

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

c

Make a choice for the QM/MM treatment of GLY   45
 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:

Enter

Make a choice for the QM/MM treatment of HIS   46
 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: 1
Give choice:

Enter

Make a choice for the QM/MM treatment of CYS  112
 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: 3
Give choice:

Enter

Make a choice for the QM/MM treatment of HIS  117
 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: 3
Give choice:

Enter

Make a choice for the QM/MM treatment of MET  121
 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: 3
Give choice:

Enter

Make a choice for the QM/MM treatment of CU   130
 0:  Put completely in QM region
 1:  Put only part of molecule in QM region

Suggestion: 0
Give choice:

Enter

Total formal charge on molecule CU    130      2.0000

Solvent molecules (SOL/HOH) belonging to this chain:
    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20
   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40
   41   42   43   44   45   46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
   61   62   63   64   65   66

Give the number of the molecule to be put in QM region (or 'c' to continue):

c

Residues belonging to chain  1

Do you want to add solvent to your system (Y/n) ?

Enter

Solvent (box) available:
   1:  HOH     HOH  Water molecule
   2:  MOH     MOH  Methanol molecule
   3:  CHL     CHL  Chloroform molecule

1

Reading contents of solvent box p2abox.HOH

Box Shape options:
 1  Spherical box
 2  Cubic box
Make a choice:

1

Writing inputfile for chain   0

Using total charge   1.0 and total spin   1.0

Maximum atomic distance (Angs) from center       25.62
Give boxsize (def.:    28.62 Angs)

30.0

Using BOXSIZE value of  30.0000
Adding atoms for box     1  Added (Box):     0 (Total):     0  Excl. (1):   648  Excl. (2):     0
Adding atoms for box     2  Added (Box):     9 (Total):     9  Excl. (1):   639  Excl. (2):     0
Adding atoms for box     3  Added (Box):     3 (Total):    12  Excl. (1):   645  Excl. (2):     0
Adding atoms for box     4  Added (Box):     0 (Total):    12  Excl. (1):   648  Excl. (2):     0
Adding atoms for box     5  Added (Box):     6 (Total):    18  Excl. (1):   642  Excl. (2):     0
Adding atoms for box     6  Added (Box):   228 (Total):   246  Excl. (1):   420  Excl. (2):     0
Adding atoms for box     7  Added (Box):   219 (Total):   465  Excl. (1):   429  Excl. (2):     0
Adding atoms for box     8  Added (Box):     9 (Total):   474  Excl. (1):   639  Excl. (2):     0
Adding atoms for box     9  Added (Box):     0 (Total):   474  Excl. (1):   648  Excl. (2):     0
Adding atoms for box    10  Added (Box):   225 (Total):   699  Excl. (1):   423  Excl. (2):     0
Adding atoms for box    11  Added (Box):   216 (Total):   915  Excl. (1):   432  Excl. (2):     0
Adding atoms for box    12  Added (Box):     6 (Total):   921  Excl. (1):   642  Excl. (2):     0
Adding atoms for box    13  Added (Box):     0 (Total):   921  Excl. (1):   648  Excl. (2):     0
Adding atoms for box    14  Added (Box):     6 (Total):   927  Excl. (1):   642  Excl. (2):     0
Adding atoms for box    15  Added (Box):    12 (Total):   939  Excl. (1):   636  Excl. (2):     0
Adding atoms for box    16  Added (Box):     0 (Total):   939  Excl. (1):   648  Excl. (2):     0
Adding atoms for box    17  Added (Box):    12 (Total):   951  Excl. (1):   636  Excl. (2):     0
Adding atoms for box    18  Added (Box):   210 (Total):  1161  Excl. (1):   438  Excl. (2):     0
Adding atoms for box    19  Added (Box):   219 (Total):  1380  Excl. (1):   429  Excl. (2):     0
Adding atoms for box    20  Added (Box):     3 (Total):  1383  Excl. (1):   645  Excl. (2):     0
Adding atoms for box    21  Added (Box):   216 (Total):  1599  Excl. (1):   417  Excl. (2):    15
Adding atoms for box    22  Added (Box):   381 (Total):  1980  Excl. (1):     3  Excl. (2):   264
Adding atoms for box    23  Added (Box):   261 (Total):  2241  Excl. (1):     3  Excl. (2):   384
Adding atoms for box    24  Added (Box):   183 (Total):  2424  Excl. (1):   423  Excl. (2):    42
Adding atoms for box    25  Added (Box):   189 (Total):  2613  Excl. (1):   426  Excl. (2):    33
Adding atoms for box    26  Added (Box):   186 (Total):  2799  Excl. (1):     3  Excl. (2):   459
Adding atoms for box    27  Added (Box):   351 (Total):  3150  Excl. (1):     3  Excl. (2):   294
Adding atoms for box    28  Added (Box):   222 (Total):  3372  Excl. (1):   420  Excl. (2):     6
Adding atoms for box    29  Added (Box):     9 (Total):  3381  Excl. (1):   639  Excl. (2):     0
Adding atoms for box    30  Added (Box):   162 (Total):  3543  Excl. (1):   429  Excl. (2):    57
Adding atoms for box    31  Added (Box):   219 (Total):  3762  Excl. (1):   426  Excl. (2):     3
Adding atoms for box    32  Added (Box):     6 (Total):  3768  Excl. (1):   642  Excl. (2):     0
Adding atoms for box    33  Added (Box):     6 (Total):  3774  Excl. (1):   642  Excl. (2):     0
Adding atoms for box    34  Added (Box):   219 (Total):  3993  Excl. (1):   426  Excl. (2):     3
Adding atoms for box    35  Added (Box):   216 (Total):  4209  Excl. (1):   432  Excl. (2):     0
Adding atoms for box    36  Added (Box):     6 (Total):  4215  Excl. (1):   642  Excl. (2):     0
Adding atoms for box    37  Added (Box):   219 (Total):  4434  Excl. (1):   426  Excl. (2):     3
Adding atoms for box    38  Added (Box):   279 (Total):  4713  Excl. (1):     6  Excl. (2):   363
Adding atoms for box    39  Added (Box):   231 (Total):  4944  Excl. (1):     0  Excl. (2):   417
Adding atoms for box    40  Added (Box):   195 (Total):  5139  Excl. (1):   432  Excl. (2):    21
Adding atoms for box    41  Added (Box):   231 (Total):  5370  Excl. (1):   414  Excl. (2):     3
Adding atoms for box    42  Added (Box):   324 (Total):  5694  Excl. (1):     0  Excl. (2):   324
Adding atoms for box    43  Added (Box):   408 (Total):  6102  Excl. (1):     6  Excl. (2):   234
Adding atoms for box    44  Added (Box):   204 (Total):  6306  Excl. (1):   435  Excl. (2):     9
Adding atoms for box    45  Added (Box):     6 (Total):  6312  Excl. (1):   642  Excl. (2):     0
Adding atoms for box    46  Added (Box):   177 (Total):  6489  Excl. (1):   435  Excl. (2):    36
Adding atoms for box    47  Added (Box):   219 (Total):  6708  Excl. (1):   429  Excl. (2):     0
Adding atoms for box    48  Added (Box):     6 (Total):  6714  Excl. (1):   642  Excl. (2):     0
Adding atoms for box    49  Added (Box):     0 (Total):  6714  Excl. (1):   648  Excl. (2):     0
Adding atoms for box    50  Added (Box):     3 (Total):  6717  Excl. (1):   645  Excl. (2):     0
Adding atoms for box    51  Added (Box):     6 (Total):  6723  Excl. (1):   642  Excl. (2):     0
Adding atoms for box    52  Added (Box):     0 (Total):  6723  Excl. (1):   648  Excl. (2):     0
Adding atoms for box    53  Added (Box):     9 (Total):  6732  Excl. (1):   639  Excl. (2):     0
Adding atoms for box    54  Added (Box):   222 (Total):  6954  Excl. (1):   426  Excl. (2):     0
Adding atoms for box    55  Added (Box):   213 (Total):  7167  Excl. (1):   426  Excl. (2):     9
Adding atoms for box    56  Added (Box):     6 (Total):  7173  Excl. (1):   642  Excl. (2):     0
Adding atoms for box    57  Added (Box):     3 (Total):  7176  Excl. (1):   645  Excl. (2):     0
Adding atoms for box    58  Added (Box):   219 (Total):  7395  Excl. (1):   423  Excl. (2):     6
Adding atoms for box    59  Added (Box):   219 (Total):  7614  Excl. (1):   429  Excl. (2):     0
Adding atoms for box    60  Added (Box):     6 (Total):  7620  Excl. (1):   642  Excl. (2):     0
Adding atoms for box    61  Added (Box):     0 (Total):  7620  Excl. (1):   648  Excl. (2):     0
Adding atoms for box    62  Added (Box):    12 (Total):  7632  Excl. (1):   636  Excl. (2):     0
Adding atoms for box    63  Added (Box):     3 (Total):  7635  Excl. (1):   645  Excl. (2):     0
Adding atoms for box    64  Added (Box):     0 (Total):  7635  Excl. (1):   648  Excl. (2):     0

Total spin   1.0

Writing inputfile for chain   1
There are no atoms in this chain, ignoring it

Inputfile(s) written, everything processed, work has been done.
Thank you for using the PDB2ADF program.

================================
Normal ending of PDB2ADF program
================================

Contents of the 1DYZ.pdb2adf file generated by pdb2adf

The file is not given completely, since it contains more than 9000 atoms.

#! /bin/sh

$AMSBIN/ams << eor
System
  Charge   1.0
  Atoms
    N     -1.1930    25.6890    17.1840 region=MM ForceField.Charge=.141400    ForceField.Type=N3   !     1 ALA      1 N   
    H     -0.3133    25.1929    17.1970 region=MM ForceField.Charge=.199700    ForceField.Type=H    !     2 ALA      1 H1  
    H     -1.3738    25.1438    18.0148 region=MM ForceField.Charge=.199700    ForceField.Type=H    !     3 ALA      1 H2  
    H     -1.5170    24.8559    16.7138 region=MM ForceField.Charge=.199700    ForceField.Type=H    !     4 ALA      1 H3  
    C     -1.4820    27.1340    16.8960 region=MM ForceField.Charge=.096200    ForceField.Type=CT   !     5 ALA      1 CA  
    H     -2.1350    27.2082    16.0264 region=MM ForceField.Charge=.088900    ForceField.Type=HP   !     6 ALA      1 HA  
    C     -2.1950    27.7860    18.0880 region=MM ForceField.Charge=-.059700   ForceField.Type=CT   !     7 ALA      1 CB  
    H     -1.5602    27.7210    18.9717 region=MM ForceField.Charge=.030000    ForceField.Type=HC   !     8 ALA      1 HB1 
    H     -2.3971    28.8331    17.8627 region=MM ForceField.Charge=.030000    ForceField.Type=HC   !     9 ALA      1 HB2 
    H     -3.1350    27.2677    18.2776 region=MM ForceField.Charge=.030000    ForceField.Type=HC   !    10 ALA      1 HB3 
    C     -0.1820    27.8790    16.5880 region=MM ForceField.Charge=.616300    ForceField.Type=C    !    11 ALA      1 C   
    O      0.8890    27.4920    17.0690 region=MM ForceField.Charge=-.572200   ForceField.Type=O    !    12 ALA      1 O   
    N     -0.2890    28.9420    15.7940 region=MM ForceField.Charge=-.415700   ForceField.Type=N    !    13 GLN      2 N   
    ...
    H     11.6901     6.5638    30.5231 region=MM ForceField.Charge=.271900    ForceField.Type=H    !   690 GLY     45 H   
    C     11.3760     8.5410    29.7530 region=QM ForceField.Charge=-.025200   ForceField.Type=CT   !   691 GLY     45 CA  
    H     10.9114     9.3322    30.3413 region=QM ForceField.Charge=.069800    ForceField.Type=H1   !   692 GLY     45 HA2 
    H     12.4602     8.6423    29.8009 region=QM ForceField.Charge=.069800    ForceField.Type=H1   !   693 GLY     45 HA3 
    C     10.9630     8.7450    28.3090 region=QM ForceField.Charge=.597300    ForceField.Type=C    !   694 GLY     45 C   
    O     10.8510     7.7910    27.5300 region=QM ForceField.Charge=-.567900   ForceField.Type=O    !   695 GLY     45 O   
    N     10.6890     9.9800    27.9260 region=QM ForceField.Charge=-.415700   ForceField.Type=N    !   696 HIS     46 N   
    H     10.7572    10.7382    28.5898 region=QM ForceField.Charge=.271900    ForceField.Type=H    !   697 HIS     46 H   
    C     10.2900    10.2500    26.5530 region=QM ForceField.Charge=-.058100   ForceField.Type=CT   !   698 HIS     46 CA  
    H     10.5517     9.3991    25.9240 region=QM ForceField.Charge=.136000    ForceField.Type=H1   !   699 HIS     46 HA  
    C      8.7770    10.5120    26.4440 region=QM ForceField.Charge=-.007400   ForceField.Type=CT   !   700 HIS     46 CB  
    H      8.5050    11.3473    27.0893 region=QM ForceField.Charge=.036700    ForceField.Type=HC   !   701 HIS     46 HB2 
    H      8.5229    10.7532    25.4118 region=QM ForceField.Charge=.036700    ForceField.Type=HC   !   702 HIS     46 HB3 
    C      7.9110     9.3590    26.8430 region=QM ForceField.Charge=.186800    ForceField.Type=CC   !   703 HIS     46 CG  
    N      8.0710     8.0910    26.3490 region=QM ForceField.Charge=-.543200   ForceField.Type=NB   !   704 HIS     46 ND1 
    C      7.1230     7.3010    26.8370 region=QM ForceField.Charge=.163500    ForceField.Type=CR   !   705 HIS     46 CE1 
    H      7.0894     6.2496    26.5516 region=QM ForceField.Charge=.143500    ForceField.Type=H5   !   706 HIS     46 HE1 
    N      6.3580     8.0230    27.6330 region=QM ForceField.Charge=-.279500   ForceField.Type=NA   !   707 HIS     46 NE2 
    H      5.5568     7.6742    28.1395 region=QM ForceField.Charge=.333900    ForceField.Type=H    !   708 HIS     46 HE2 
    C      6.8210     9.3110    27.6620 region=QM ForceField.Charge=-.220700   ForceField.Type=CW   !   709 HIS     46 CD2 
    H      6.3141    10.0588    28.2719 region=QM ForceField.Charge=.186200    ForceField.Type=H4   !   710 HIS     46 HD2 
    C     10.9790    11.4950    26.0450 region=MM ForceField.Charge=.597300    ForceField.Type=C    !   711 HIS     46 C   
    ...
    C     11.0290     8.8020    20.9600 region=QM ForceField.Charge=.035000    ForceField.Type=CT   !  1648 CYS    112 CA  
    H     11.3902     9.8061    21.1823 region=QM ForceField.Charge=.048000    ForceField.Type=H1   !  1649 CYS    112 HA  
    C     10.0620     8.3640    22.0630 region=QM ForceField.Charge=-.736000   ForceField.Type=CT   !  1650 CYS    112 CB  
    H      9.2477     9.0845    22.1402 region=QM ForceField.Charge=.244000    ForceField.Type=H1   !  1651 CYS    112 HB3 
    H      9.6557     7.3817    21.8218 region=QM ForceField.Charge=.244000    ForceField.Type=H1   !  1652 CYS    112 HB2 
    S     10.8340     8.2410    23.7100 region=QM ForceField.Charge=-.736000   ForceField.Type=SH   !  1653 CYS    112 SG  
    C     10.1650     3.3080    22.4340 region=QM ForceField.Charge=-.058100   ForceField.Type=CT   !  1710 HIS    117 CA  
    H      9.2929     2.7403    22.7584 region=QM ForceField.Charge=.136000    ForceField.Type=H1   !  1711 HIS    117 HA  
    C     10.1750     4.6030    23.2620 region=QM ForceField.Charge=-.007400   ForceField.Type=CT   !  1712 HIS    117 CB  
    H     11.1220     5.1220    23.1143 region=QM ForceField.Charge=.036700    ForceField.Type=HC   !  1713 HIS    117 HB2 
    H      9.3551     5.2459    22.9418 region=QM ForceField.Charge=.036700    ForceField.Type=HC   !  1714 HIS    117 HB3 
    C     10.0160     4.3980    24.7440 region=QM ForceField.Charge=.186800    ForceField.Type=CC   !  1715 HIS    117 CG  
    N      9.7040     5.4090    25.6080 region=QM ForceField.Charge=-.543200   ForceField.Type=NB   !  1716 HIS    117 ND1 
    C      9.6570     4.9300    26.8540 region=QM ForceField.Charge=.163500    ForceField.Type=CR   !  1717 HIS    117 CE1 
    H      9.4228     5.5952    27.6851 region=QM ForceField.Charge=.143500    ForceField.Type=H5   !  1718 HIS    117 HE1 
    N      9.9280     3.6450    26.8000 region=QM ForceField.Charge=-.279500   ForceField.Type=NA   !  1719 HIS    117 NE2 
    H      9.9617     3.0260    27.5974 region=QM ForceField.Charge=.333900    ForceField.Type=H    !  1720 HIS    117 HE2 
    C     10.1580     3.2710    25.4990 region=QM ForceField.Charge=-.220700   ForceField.Type=CW   !  1721 HIS    117 CD2 
    H     10.3982     2.2340    25.2644 region=QM ForceField.Charge=.186200    ForceField.Type=H4   !  1722 HIS    117 HD2 
    C      6.0350     6.2800    19.5280 region=QM ForceField.Charge=-.023700   ForceField.Type=CT   !  1778 MET    121 CA  
    H      4.9702     6.5113    19.5559 region=QM ForceField.Charge=.088000    ForceField.Type=H1   !  1779 MET    121 HA  
    C      6.6730     6.7710    20.8330 region=QM ForceField.Charge=.034200    ForceField.Type=CT   !  1780 MET    121 CB  
    H      7.7511     6.6157    20.7919 region=QM ForceField.Charge=.024100    ForceField.Type=HC   !  1781 MET    121 HB2 
    H      6.4641     7.8329    20.9631 region=QM ForceField.Charge=.024100    ForceField.Type=HC   !  1782 MET    121 HB3 
    C      6.1560     6.0500    22.0720 region=QM ForceField.Charge=.001800    ForceField.Type=CT   !  1783 MET    121 CG  
    H      5.0693     6.1257    22.1101 region=QM ForceField.Charge=.044000    ForceField.Type=H1   !  1784 MET    121 HG2 
    H      6.4453     5.0000    22.0292 region=QM ForceField.Charge=.044000    ForceField.Type=H1   !  1785 MET    121 HG3 
    S      6.7760     6.6970    23.6140 region=QM ForceField.Charge=-.273700   ForceField.Type=S    !  1786 MET    121 SD  
    C      6.0690     8.3070    23.6050 region=QM ForceField.Charge=-.053600   ForceField.Type=CT   !  1787 MET    121 CE  
    H      4.9825     8.2271    23.5709 region=QM ForceField.Charge=.068400    ForceField.Type=H1   !  1788 MET    121 HE1 
    H      6.3654     8.8396    24.5086 region=QM ForceField.Charge=.068400    ForceField.Type=H1   !  1789 MET    121 HE2 
    H      6.4202     8.8537    22.7299 region=QM ForceField.Charge=.068400    ForceField.Type=H1   !  1790 MET    121 HE3 
    CU     9.5640     7.3450    25.1750 region=QM ForceField.Charge=2.000000   ForceField.Type=CU   !  1915 CU     130 CU  
    ...
    O     31.1328    34.4612    22.6903 region=MM ForceField.Charge=-.834000   ForceField.Type=OW   !  9746 HOH  2545 O   
    H     31.8908    34.5740    22.1167 region=MM ForceField.Charge=.417000    ForceField.Type=HW   !  9747 HOH  2545 H1  
    H     30.6706    35.2981    22.6446 region=MM ForceField.Charge=.417000    ForceField.Type=HW   !  9748 HOH  2545 H2  
  End

  BondOrders
        1      5 1.0
        1      2 1.0
        1      3 1.0
        1      4 1.0
        5      7 1.0
        5     11 1.0
        5      6 1.0
        7      8 1.0
        7      9 1.0
        7     10 1.0
       11     12 1.0
       11     13 1.0
       13     15 1.0
       13     14 1.0
       15     17 1.0
       15     28 1.0
       15     16 1.0
       17     20 1.0
       17     18 1.0
       17     19 1.0
     ...
     9746   9747 1.0
     9746   9748 1.0
  End
End

Task GeometryOptimization

GeometryOptimization
  MaxIterations 100
  Convergence Gradients=1e-3
End
Engine Hybrid
  QMMM QMRegion=QM QMEngineID=ADF MMEngineID=ForceField

  Capping
    AtomicInfoForCappingAtom ForceField.Type=H1 ForceField.Charge=0.0
  End
  Engine ADF
    Title QM/MM calculation setup by pdb2adf: M.Swart et al., 2020
    Symmetry NOSYM

    Eprint
      SFO NOEIG NOOVL
    End

    XC
      GGA BP86
    End

    Basis
      type TZP
      core small
    End

    SCF
      diis ok=0.01
      Converge 1.0e-5 1.0e-5
      Iterations 99
    End
    Unrestricted
    SpinPolarization   1.0
  EndEngine
  Engine ForceField
    Type Amber95
    ForceFieldFile $AMSHOME/atomicdata/ForceFields/amber95.ff
  EndEngine
EndEngine
eor

An example on solvent shell run

The idea of this example is to make an adf-input file using a PDB file of water (hoh.pdb.txt), in the solvent methanol. The water molecule in the adf-input file should be in the QM part, and the solvent methanol (in a box) is in MM part.

Contents of the hoh.pdb file

TITLE     PDB-FILE CORRESPONDING TO pdb2adf-GENERATED ADF-INPUTFILE
REMARK    Written by M. Swart, March 2005
HETATM    1 H1   HOH     1       1.716  26.282  11.239  1.00  0.00      1DYZ H
HETATM    2 O    HOH     1       2.439  25.795  11.634  1.00  0.00      1DYZ O
HETATM    3 H2   HOH     1       3.140  26.440  11.729  1.00  0.00      1DYZ H
END   

Usage of pdb2adf

The program works interactively. Given below in bold are the parts that the user has to type. In cases where the user agrees with the suggestion given by the program, the user can press the Enter key indicated with Enter.

                                  P D B 2 A D F - program
                                     version 2008.01
                              Written by: Marcel Swart, 2008

                         This program uses AMBER parameter files
                            see: http://amber.scripps.edu
Please give name of PDB-file

hoh.pdb.txt

Do you want a logfile to be written (Y/n) ?

Enter

 read fragments

Data Processed:
     Nat:          3
    Nmol:          1
 NChains:          0

Please wait, making connection tables
Now finding nearby atoms
Assigning chain ID to all residues
Completing residues for which only option is available

Refinding nearby atoms (including atoms added in residue completion)

 - - - - - - - - - - - - - - - - - - - - - - - - - - -
           Making Choices for Chain      0
 - - - - - - - - - - - - - - - - - - - - - - - - - - -

Completing residues with multiple options available, and solvent molecules

Checking positions of newly added atoms

Making choice for which molecules should be QM, which MM

Residues belonging to chain  0

Solvent molecules (SOL/HOH) belonging to this chain:
    1

Give the number of the molecule to be put in QM region (or 'c' to continue):

1

Putting HOH    1 in QM region

Give the number of the molecule to be put in QM region (or 'c' to continue):

c

Do you want to add solvent to your system (Y/n) ?

Enter

Solvent (box) available:
   1:  HOH     HOH  Water molecule
   2:  MOH     MOH  Methanol molecule
   3:  CHL     CHL  Chloroform molecule

2

Reading contents of solvent box p2abox.MOH

Box Shape options:
 1  Spherical box
 2  Cubic box
Make a choice:

1

Writing inputfile for chain   0

Using total charge   0.0 and total spin   0.0

Maximum atomic distance (Angs) from center        0.92
Give boxsize (def.:    15.00 Angs)

14.0

Using BOXSIZE value of  14.0000
Adding atoms for box     1  Added (Box):    84 (Total):    84  Excl. (1):   660  Excl. (2):     6
Adding atoms for box     2  Added (Box):   102 (Total):   186  Excl. (1):   642  Excl. (2):     6
Adding atoms for box     3  Added (Box):   102 (Total):   288  Excl. (1):   642  Excl. (2):     6
Adding atoms for box     4  Added (Box):   108 (Total):   396  Excl. (1):   642  Excl. (2):     0
Adding atoms for box     5  Added (Box):   120 (Total):   516  Excl. (1):   630  Excl. (2):     0
Adding atoms for box     6  Added (Box):    96 (Total):   612  Excl. (1):   654  Excl. (2):     0
Adding atoms for box     7  Added (Box):   108 (Total):   720  Excl. (1):   642  Excl. (2):     0
Adding atoms for box     8  Added (Box):   102 (Total):   822  Excl. (1):   642  Excl. (2):     6

Inputfile(s) written, everything processed, work has been done.
Thank you for using the PDB2ADF program.

================================
Normal ending of PDB2ADF program
================================

Contents of the hoh.pdb2adf file generated by pdb2adf

The file is not given completely, since it contains more than 800 atoms.

#! /bin/sh

$AMSBIN/ams << eor
System
  Charge   0.0
  Atoms
    O      2.4390    25.7950    11.6340 region=QM ForceField.Charge=-.834000   ForceField.Type=OW   !     1 HOH      1 O   
    H      1.7160    26.2820    11.2390 region=QM ForceField.Charge=.417000    ForceField.Type=HW   !     2 HOH      1 H1  
    H      3.1400    26.4400    11.7290 region=QM ForceField.Charge=.417000    ForceField.Type=HW   !     3 HOH      1 H2  
    C    -10.0667    22.2493    11.7437 region=MM ForceField.Charge=.116600    ForceField.Type=CT   !     4 MOH     1 C1  
    H    -10.2077    21.5053    10.9597 region=MM ForceField.Charge=.037200    ForceField.Type=H1   !     5 MOH     1 HC1 
    H    -10.5047    21.8683    12.6667 region=MM ForceField.Charge=.037200    ForceField.Type=H1   !     6 MOH     1 HC2 
    H    -10.5167    23.2103    11.4977 region=MM ForceField.Charge=.037200    ForceField.Type=H1   !     7 MOH     1 HC3 
    O     -8.7387    22.3983    12.0617 region=MM ForceField.Charge=-.649700   ForceField.Type=OH   !     8 MOH     1 O1  
    H     -8.3007    22.6943    11.2607 region=MM ForceField.Charge=.421500    ForceField.Type=HO   !     9 MOH     1 HO1 
    C     -0.2827    19.0253     2.2847 region=MM ForceField.Charge=.116600    ForceField.Type=CT   !    10 MOH     2 C1  
    H     -0.5357    18.2063     2.9567 region=MM ForceField.Charge=.037200    ForceField.Type=H1   !    11 MOH     2 HC1 
    H      0.7633    19.2913     2.4407 region=MM ForceField.Charge=.037200    ForceField.Type=H1   !    12 MOH     2 HC2 
    H     -0.9267    19.8753     2.5107 region=MM ForceField.Charge=.037200    ForceField.Type=H1   !    13 MOH     2 HC3 
    O     -0.4997    18.6373     0.9467 region=MM ForceField.Charge=-.649700   ForceField.Type=OH   !    14 MOH     2 O1  
    H      0.1123    17.9313     0.7287 region=MM ForceField.Charge=.421500    ForceField.Type=HO   !    15 MOH     2 HO1 
    ...
    C      6.1721    28.5021    18.9485 region=MM ForceField.Charge=.116600    ForceField.Type=CT   !   820 MOH   137 C1  
    H      7.1011    27.9431    18.8355 region=MM ForceField.Charge=.037200    ForceField.Type=H1   !   821 MOH   137 HC1 
    H      6.3621    29.4771    19.3985 region=MM ForceField.Charge=.037200    ForceField.Type=H1   !   822 MOH   137 HC2 
    H      5.4711    27.9401    19.5645 region=MM ForceField.Charge=.037200    ForceField.Type=H1   !   823 MOH   137 HC3 
    O      5.5611    28.7181    17.7095 region=MM ForceField.Charge=-.649700   ForceField.Type=OH   !   824 MOH   137 O1  
    H      5.2631    27.8621    17.3935 region=MM ForceField.Charge=.421500    ForceField.Type=HO   !   825 MOH   137 HO1 
  End

  BondOrders
        1      2 1.0
        1      3 1.0
        4      5 1.0
        4      6 1.0
        4      7 1.0
        4      8 1.0
        8      9 1.0
       10     11 1.0
       10     12 1.0
       10     13 1.0
       10     14 1.0
       14     15 1.0
      ...
      820    821 1.0
      820    822 1.0
      820    823 1.0
      820    824 1.0
      824    825 1.0
  End
End

Task GeometryOptimization

GeometryOptimization
  MaxIterations 100
  Convergence Gradients=1e-3
End
Engine Hybrid
  QMMM QMRegion=QM QMEngineID=ADF MMEngineID=ForceField

  Capping
    AtomicInfoForCappingAtom ForceField.Type=H1 ForceField.Charge=0.0
  End
  Engine ADF
    Title QM/MM calculation setup by pdb2adf: M.Swart et al., 2020
    Symmetry NOSYM

    Eprint
      SFO NOEIG NOOVL
    End

    XC
      GGA BP86
    End

    Basis
      type TZP
      core small
    End

    SCF
      diis ok=0.01
      Converge 1.0e-5 1.0e-5
      Iterations 99
    End
  EndEngine
  Engine ForceField
    Type Amber95
    ForceFieldFile $AMSHOME/atomicdata/ForceFields/amber95.ff
  EndEngine
EndEngine
eor