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.
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