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 NEWQMMM format is used if the environment variable SCM_PDB2ADF is set to NEW. By default the ‘old’ QM/MM input style 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 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) ?
Please give name of PDB-file
Found the following terminal amino acid residues : (C-term) 10 (N-term) 1 Do you want to use these as terminal residues (Y/n) ?
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
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
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
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
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:
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:
Do you want to add solvent to your system (Y/n) ?
Solvent (box) available: 1: HOH HOH Water molecule 2: MOH MOH Methanol molecule 3: CHL CHL Chloroform molecule
Make a choice:
Give boxsize (def.: 16.71 Angs)