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.
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
4 5
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.
Do you want a logfile to be written (Y/n) ?
Enter
Please give name of PDB-file
chymotrypsin.pdb
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
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 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
Make a choice:
1
Give boxsize (def.: 16.71 Angs)
17.5