Contents of the 1DYZ.pdb2adf file generated by pdb2adf
The file is not given completely, since it contains more than 9000 atoms.
#! /bin/sh
$ADFBIN/adf << eor
TITLE QM/MM calculation setup by pdb2adf: M.Swart, 2005
Symmetry NOSYM
EPRINT
SFO NOEIG NOOVL
END
XC
GGA Becke-Perdew
END
GEOMETRY
CONVERGE grad=1.0e-3 rad=1.0e-1
END
BASIS
type TZP
core small
END
SCF
Converge 1.0e-5 1.0e-5
Iterations 99
END
INTEGRATION 5.0 5.0 5.0
CHARGE 1.0 1.0
UNRESTRICTED
ATOMS
1 C 11.3760 8.5410 29.7530
2 H 10.9114 9.3322 30.3413
3 H 12.4602 8.6423 29.8009
4 C 10.9630 8.7450 28.3090
5 O 10.8510 7.7910 27.5300
6 N 10.6890 9.9800 27.9260
7 H 10.7572 10.7382 28.5898
8 C 10.2900 10.2500 26.5530
9 H 10.5517 9.3991 25.9240
10 C 8.7770 10.5120 26.4440
11 H 8.5050 11.3473 27.0893
12 H 8.5229 10.7532 25.4118
13 C 7.9110 9.3590 26.8430
14 N 8.0710 8.0910 26.3490
15 C 7.1230 7.3010 26.8370
16 H 7.0894 6.2496 26.5516
17 N 6.3580 8.0230 27.6330
18 H 5.5568 7.6742 28.1395
19 C 6.8210 9.3110 27.6620
20 H 6.3141 10.0588 28.2719
21 C 11.0290 8.8020 20.9600
22 H 11.3902 9.8061 21.1823
23 C 10.0620 8.3640 22.0630
24 H 9.2477 9.0845 22.1402
25 H 9.6557 7.3817 21.8218
26 S 10.8340 8.2410 23.7100
27 C 10.1650 3.3080 22.4340
28 H 9.2929 2.7403 22.7584
29 C 10.1750 4.6030 23.2620
30 H 11.1220 5.1220 23.1143
31 H 9.3551 5.2459 22.9418
32 C 10.0160 4.3980 24.7440
33 N 9.7040 5.4090 25.6080
34 C 9.6570 4.9300 26.8540
35 H 9.4228 5.5952 27.6851
36 N 9.9280 3.6450 26.8000
37 H 9.9617 3.0260 27.5974
38 C 10.1580 3.2710 25.4990
39 H 10.3982 2.2340 25.2644
40 C 6.0350 6.2800 19.5280
41 H 4.9702 6.5113 19.5559
42 C 6.6730 6.7710 20.8330
43 H 7.7511 6.6157 20.7919
44 H 6.4641 7.8329 20.9631
45 C 6.1560 6.0500 22.0720
46 H 5.0693 6.1257 22.1101
47 H 6.4453 5.0000 22.0292
48 S 6.7760 6.6970 23.6140
49 C 6.0690 8.3070 23.6050
50 H 4.9825 8.2271 23.5709
51 H 6.3654 8.8396 24.5086
52 H 6.4202 8.8537 22.7299
53 CU 9.5640 7.3450 25.1750
54 N 10.9860 7.2480 30.2860
55 C 10.9790 11.4950 26.0450
56 N 10.3490 8.8040 19.6720
57 C 12.2010 7.8400 20.8870
58 N 11.3800 2.5190 22.6730
59 C 9.8250 3.6710 20.9970
60 N 6.2160 4.8460 19.4030
61 C 6.6330 7.0040 18.3530
62 N -1.1930 25.6890 17.1840
63 H -0.3133 25.1929 17.1970
64 H -1.3738 25.1438 18.0148
65 H -1.5170 24.8559 16.7138
66 C -1.4820 27.1340 16.8960
67 H -2.1350 27.2082 16.0264
68 C -2.1950 27.7860 18.0880
69 H -1.5602 27.7210 18.9717
70 H -2.3971 28.8331 17.8627
71 H -3.1350 27.2677 18.2776
72 C -0.1820 27.8790 16.5880
73 O 0.8890 27.4920 17.0690
74 N -0.2890 28.9420 15.7940
75 H -1.1936 29.2105 15.4339
76 C 0.8750 29.7430 15.4220
77 H 0.5616 30.5606 14.7728
78 C 1.5270 30.3290 16.6860
...
9746 O 31.1328 34.4612 22.6903
9747 H 31.8908 34.5740 22.1167
9748 H 30.6706 35.2981 22.6446
END
QMMM
FORCE_FIELD_FILE $ADFRESOURCES/ForceFields/amber95.ff
RESTART_FILE mm.restart ! old style restart
OUTPUT_LEVEL=1
WARNING_LEVEL=0
! -------------------
! for AddRemove model
! -------------------
PARTITION=5
ELSTAT_COUPLING_MODEL=4 ! for AddRemove model
OPTIMIZE
METHOD CONJGRAD
MAX_STEPS 5000
PRINT_CYCLES 10
MM_NOTCONVERGED 0
SUBEND
LINK_BONDS
1 - 54 1.3320 H H1
8 - 55 1.3861 H H1
21 - 56 1.3362 H H1
21 - 57 1.3927 H H1
27 - 58 1.3471 H H1
27 - 59 1.3951 H H1
40 - 60 1.3310 H H1
40 - 61 1.3799 H H1
SUBEND
MM_CONNECTION_TABLE
1 CT QM 54 4 2 3
2 H1 QM 1
3 H1 QM 1
4 C QM 1 5 6
5 O QM 4
6 N QM 8 4 7
7 H QM 6
8 CT QM 6 10 55 9
9 H1 QM 8
10 CT QM 8 13 11 12
11 HC QM 10
12 HC QM 10
13 CC QM 10 14 19
14 NB QM 13 15 53
15 CR QM 14 17 16
16 H5 QM 15
17 NA QM 15 19 18
18 H QM 17
19 CW QM 13 17 20
20 H4 QM 19
21 CT QM 56 23 57 22
22 H1 QM 21
23 CT QM 21 26 24 25
24 H1 QM 23
25 H1 QM 23
26 SH QM 23 53
27 CT QM 58 29 59 28
28 H1 QM 27
29 CT QM 27 32 30 31
30 HC QM 29
31 HC QM 29
32 CC QM 29 33 38
33 NB QM 32 34 53
34 CR QM 33 36 35
35 H5 QM 34
36 NA QM 34 38 37
37 H QM 36
38 CW QM 32 36 39
39 H4 QM 38
40 CT QM 60 42 61 41
41 H1 QM 40
42 CT QM 40 45 43 44
43 HC QM 42
44 HC QM 42
45 CT QM 42 48 46 47
46 H1 QM 45
47 H1 QM 45
48 S QM 45 49
49 CT QM 48 50 51 52
50 H1 QM 49
51 H1 QM 49
52 H1 QM 49
53 CU QM 14 26 33
54 N LI 1 748 750
55 C LI 8 751 752
56 N LI 21 1683 1685
57 C LI 21 1686 1687
58 N LI 27 1737 1739
59 C LI 27 1740 1741
60 N LI 40 1790 1792
61 C LI 40 1793 1794
62 N3 MM 66 63 64 65
63 H MM 62
64 H MM 62
65 H MM 62
66 CT MM 62 68 72 67
67 HP MM 66
68 CT MM 66 69 70 71
69 HC MM 68
70 HC MM 68
71 HC MM 68
72 C MM 66 73 74
73 O MM 72
74 N MM 76 72 75
75 H MM 74
76 CT MM 74 78 89 77
77 H1 MM 76
78 CT MM 76 81 79 80
....
9746 OW MM 9747 9748
9747 HW MM 9746
9748 HW MM 9746
SUBEND
CHARGES
1 -0.0252
2 0.0698
3 0.0698
4 0.5973
5 -0.5679
6 -0.4157
7 0.2719
8 -0.0581
9 0.1360
10 -0.0074
11 0.0367
12 0.0367
13 0.1868
14 -0.5432
15 0.1635
16 0.1435
17 -0.2795
18 0.3339
19 -0.2207
20 0.1862
21 0.0350
22 0.0480
23 -0.7360
24 0.2440
25 0.2440
26 -0.7360
27 -0.0581
28 0.1360
29 -0.0074
30 0.0367
31 0.0367
32 0.1868
33 -0.5432
34 0.1635
35 0.1435
36 -0.2795
37 0.3339
38 -0.2207
39 0.1862
40 -0.0237
41 0.0880
42 0.0342
43 0.0241
44 0.0241
45 0.0018
46 0.0440
47 0.0440
48 -0.2737
49 -0.0536
50 0.0684
51 0.0684
52 0.0684
53 2.0000
54 -0.4157
55 0.5973
56 -0.4630
57 0.6160
58 -0.4157
59 0.5973
60 -0.4157
61 0.5973
62 0.1414
63 0.1997
64 0.1997
65 0.1997
66 0.0962
67 0.0889
68 -0.0597
69 0.0300
70 0.0300
71 0.0300
72 0.6163
73 -0.5722
74 -0.4157
75 0.2719
76 -0.0031
77 0.0850
78 -0.0036
....
9746 -0.8340
9747 0.4170
9748 0.4170
SUBEND
END
COMMENT
Atom ADF ID p2a ID Amber Mol Nr Amber pdb ID atom
C 1 828 CT GLY 45 GLY 338 CA
H 2 829 H1 GLY 45 GLY 0 HA2
H 3 830 H1 GLY 45 GLY 0 HA3
C 4 831 C GLY 45 GLY 339 C
O 5 832 O GLY 45 GLY 340 O
N 6 836 N HIS 46 HIE 341 N
H 7 837 H HIS 46 HIE 0 H
C 8 838 CT HIS 46 HIE 342 CA
H 9 839 H1 HIS 46 HIE 0 HA
C 10 840 CT HIS 46 HIE 345 CB
H 11 841 HC HIS 46 HIE 0 HB2
H 12 842 HC HIS 46 HIE 0 HB3
C 13 843 CC HIS 46 HIE 346 CG
N 14 844 NB HIS 46 HIE 347 ND1
C 15 846 CR HIS 46 HIE 349 CE1
C 15 846 CR HIS 46 HIE 349 CE1
H 16 847 H5 HIS 46 HIE 0 HE1
N 17 848 NA HIS 46 HIE 350 NE2
H 18 849 H HIS 46 HIE 0 HE2
C 19 850 CW HIS 46 HIE 348 CD2
H 20 851 H4 HIS 46 HIE 0 HD2
C 21 1996 CT CYS 112 CYM 824 CA
H 22 1997 H1 CYS 112 CYM 0 HA
C 23 1998 CT CYS 112 CYM 827 CB
H 24 1999 H1 CYS 112 CYM 0 HB3
H 25 2000 H1 CYS 112 CYM 0 HB2
S 26 2001 SH CYS 112 CYM 828 SG
C 27 2074 CT HIS 117 HIE 858 CA
H 28 2075 H1 HIS 117 HIE 0 HA
C 29 2076 CT HIS 117 HIE 861 CB
H 30 2077 HC HIS 117 HIE 0 HB2
H 31 2078 HC HIS 117 HIE 0 HB3
C 32 2079 CC HIS 117 HIE 862 CG
N 33 2080 NB HIS 117 HIE 863 ND1
C 34 2082 CR HIS 117 HIE 865 CE1
H 35 2083 H5 HIS 117 HIE 0 HE1
N 36 2084 NA HIS 117 HIE 866 NE2
H 37 2085 H HIS 117 HIE 0 HE2
C 38 2086 CW HIS 117 HIE 864 CD2
H 39 2087 H4 HIS 117 HIE 0 HD2
C 40 2155 CT MET 121 MET 895 CA
H 41 2156 H1 MET 121 MET 0 HA
C 42 2157 CT MET 121 MET 898 CB
H 43 2158 HC MET 121 MET 0 HB2
H 44 2159 HC MET 121 MET 0 HB3
C 45 2160 CT MET 121 MET 899 CG
H 46 2161 H1 MET 121 MET 0 HG2
H 47 2162 H1 MET 121 MET 0 HG3
S 48 2163 S MET 121 MET 900 SD
C 49 2164 CT MET 121 MET 901 CE
H 50 2165 H1 MET 121 MET 0 HE1
H 51 2166 H1 MET 121 MET 0 HE2
H 52 2167 H1 MET 121 MET 0 HE3
CU 53 2318 CU CU 130 959 CU
N 54 826 N GLY 45 GLY 337 N
C 55 852 C HIS 46 HIE 343 C
N 56 1994 N CYS 112 CYM 823 N
C 57 2003 C CYS 112 CYM 825 C
N 58 2072 N HIS 117 HIE 857 N
C 59 2088 C HIS 117 HIE 859 C
N 60 2153 N MET 121 MET 894 N
C 61 2168 C MET 121 MET 896 C
N 62 1 N3 ALA 1 ALA 1 N
H 63 2 H ALA 1 ALA 0 H1
H 64 11 H ALA 1 ALA 0 H2
H 65 12 H ALA 1 ALA 0 H3
C 66 3 CT ALA 1 ALA 2 CA
H 67 4 HP ALA 1 ALA 0 HA
C 68 5 CT ALA 1 ALA 5 CB
H 69 6 HC ALA 1 ALA 0 HB1
H 70 7 HC ALA 1 ALA 0 HB2
H 71 8 HC ALA 1 ALA 0 HB3
C 72 9 C ALA 1 ALA 3 C
O 73 10 O ALA 1 ALA 4 O
N 74 14 N GLN 2 GLN 6 N
H 75 15 H GLN 2 GLN 0 H
C 76 16 CT GLN 2 GLN 7 CA
H 77 17 H1 GLN 2 GLN 0 HA
C 78 18 CT GLN 2 GLN 10 CB
....
O 2111 2517 OW HOH 196 SOL 1025 O
H 2112 2518 HW HOH 196 SOL 0 H1
H 2113 2519 HW HOH 196 SOL 0 H2
END
ENDINPUT
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