Example in $ADFHOME/examples/adf

Shown here ia a pdb2adf example that is stored in the subdirectories under $ADFHOME/examples/adf, where $ADFHOME is the main directory of the ADF package.

pdb2adf: transforms a PDB file in a QM/MM adf-input file

Sample directory: adf/pdb2adf/

This example shows how to use the utiliy pdb2adf, which creates an ADF input file from a PDB file, for a subsequent QM/MM calculation using ADF. Note that the old style QM/MM input format is used if the environment variable SCM_PDB2ADF is set to OLD. By default the NEWQMMM input format is used.

First create the PDB file that can be used in this example.

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     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 the pdf2adf program to create ADF inputfile

$ADFBIN/pdb2adf << eor
chymotrypsin.pdb




3 4 5
c
5
3 4 15 16
c


Y
1
1
17.5
eor

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.

The questions asked can be found in the output file, and are repeated here. The Enter key or empty line is indicated here with Enter.

Please give name of PDB-file

chymotrypsin.pdb

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

Enter

...
Found the following terminal amino acid residues : (C-term)    10 (N-term)     1
Do you want to use these as terminal residues (Y/n) ?

Enter

...
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

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

  Connections and Nearest Atoms for SG CYS    1 SG  ( P2A #    8 PDB#    6 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.83       5       5  CB  CYS    1  CB       1       5.58      19       0  H1  GLY    2
                                                   2       6.06      36       0  HC  VAL    3
                                                   3       6.09      26       0  H   VAL    3
                                                   4       6.47      25      11  N   VAL    3  N
                                                   5       7.15      35      17  CT  VAL    3  CG2
Suggestion: 1

Enter

...
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

3 4 5

...
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 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:

5

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)

3 4 15 16

...
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)

c

Make a choice for the QM/MM treatment of PRO    4
 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 ALA    5
 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

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

Y

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

1

Box Shape options:
 1  Spherical box
 2  Cubic box

Make a choice:

1

Give boxsize (def.:    16.71 Angs)

17.5