Setting up calculation model
Prepare Oxytocin model
You can get Oxytocin model from here.
Or you save the following text as 1NPO_model.pdb.
REMARK
ATOM 1 N CYS 1 9.331 11.830 15.518
ATOM 2 H1 CYS 1 9.177 10.832 15.477
ATOM 3 H2 CYS 1 10.131 11.987 16.113
ATOM 4 H3 CYS 1 8.520 12.263 15.935
ATOM 5 CA CYS 1 9.613 12.372 14.179
ATOM 6 HA CYS 1 8.780 12.081 13.538
ATOM 7 CB CYS 1 9.762 13.910 14.219
ATOM 8 2HB CYS 1 9.797 14.294 13.200
ATOM 9 3HB CYS 1 8.898 14.363 14.706
ATOM 10 SG CYS 1 11.222 14.496 15.123
ATOM 11 C CYS 1 10.890 11.737 13.616
ATOM 12 O CYS 1 11.675 11.153 14.361
ATOM 13 X CYS 1 8.862 10.671 18.277 -1.00
ATOM 14 N TYR 2 11.171 11.934 12.329
ATOM 15 H TYR 2 10.442 12.332 11.755
ATOM 16 CA TYR 2 12.407 11.582 11.631
ATOM 17 HA TYR 2 13.142 11.307 12.387
ATOM 18 CB TYR 2 12.142 10.373 10.701
ATOM 19 2HB TYR 2 11.565 10.703 9.838
ATOM 20 3HB TYR 2 13.115 10.035 10.343
ATOM 21 CG TYR 2 11.470 9.143 11.291
ATOM 22 CD1 TYR 2 12.008 8.595 12.466
ATOM 23 HD1 TYR 2 12.829 9.081 12.971
ATOM 24 CE1 TYR 2 11.515 7.394 12.978
ATOM 25 HE1 TYR 2 11.948 6.944 13.859
ATOM 26 CZ TYR 2 10.485 6.729 12.317
ATOM 27 OH TYR 2 10.104 5.571 12.869
ATOM 28 HH TYR 2 9.514 5.095 12.280
ATOM 29 CE2 TYR 2 9.913 7.258 11.139
ATOM 30 HE2 TYR 2 9.118 6.728 10.636
ATOM 31 CD2 TYR 2 10.414 8.473 10.624
ATOM 32 HD2 TYR 2 10.002 8.872 9.709
ATOM 33 C TYR 2 12.967 12.782 10.812
ATOM 34 O TYR 2 12.252 13.760 10.585
ATOM 35 N ILE 3 14.223 12.718 10.344
ATOM 36 H ILE 3 14.762 11.934 10.682
ATOM 37 CA ILE 3 14.962 13.698 9.496
ATOM 38 HA ILE 3 15.212 14.522 10.165
ATOM 39 CB ILE 3 16.342 13.104 9.044
ATOM 40 HB ILE 3 16.929 12.908 9.942
ATOM 41 CG2 ILE 3 16.213 11.761 8.313
ATOM 42 1HG2 ILE 3 15.603 11.056 8.879
ATOM 43 2HG2 ILE 3 15.771 11.926 7.331
ATOM 44 3HG2 ILE 3 17.205 11.323 8.195
ATOM 45 CG1 ILE 3 17.230 14.008 8.155
ATOM 46 2HG1 ILE 3 18.157 13.489 7.911
ATOM 47 3HG1 ILE 3 16.735 14.211 7.205
ATOM 48 CD1 ILE 3 17.615 15.320 8.843
ATOM 49 1HD1 ILE 3 16.760 15.995 8.889
ATOM 50 2HD1 ILE 3 17.963 15.117 9.855
ATOM 51 3HD1 ILE 3 18.418 15.795 8.278
ATOM 52 C ILE 3 14.169 14.397 8.349
ATOM 53 O ILE 3 14.515 15.518 7.985
ATOM 54 N GLN 4 13.059 13.870 7.813
ATOM 55 H GLN 4 12.803 12.938 8.104
ATOM 56 CA GLN 4 12.187 14.595 6.847
ATOM 57 HA GLN 4 12.819 15.095 6.113
ATOM 58 CB GLN 4 11.232 13.656 6.087
ATOM 59 2HB GLN 4 10.852 12.879 6.751
ATOM 60 3HB GLN 4 10.387 14.229 5.706
ATOM 61 CG GLN 4 11.941 13.077 4.865
ATOM 62 2HG GLN 4 12.213 13.899 4.203
ATOM 63 3HG GLN 4 12.859 12.603 5.212
ATOM 64 CD GLN 4 11.115 12.078 4.051
ATOM 65 OE1 GLN 4 9.904 12.174 3.867
ATOM 66 NE2 GLN 4 11.769 11.081 3.510
ATOM 67 1HE2 GLN 4 11.290 10.327 3.038
ATOM 68 2HE2 GLN 4 12.777 11.093 3.574
ATOM 69 C GLN 4 11.317 15.696 7.457
ATOM 70 O GLN 4 10.818 16.553 6.723
ATOM 71 N ASN 5 11.093 15.665 8.770
ATOM 72 H ASN 5 11.532 14.942 9.322
ATOM 73 CA ASN 5 10.123 16.553 9.390
ATOM 74 HA ASN 5 10.089 17.464 8.793
ATOM 75 CB ASN 5 8.728 15.910 9.283
ATOM 76 2HB ASN 5 8.555 15.544 8.270
ATOM 77 3HB ASN 5 8.637 15.064 9.965
ATOM 78 CG ASN 5 7.674 16.960 9.575
ATOM 79 OD1 ASN 5 7.717 18.077 9.076
ATOM 80 ND2 ASN 5 6.743 16.678 10.449
ATOM 81 1HD2 ASN 5 6.111 17.421 10.711
ATOM 82 2HD2 ASN 5 6.674 15.744 10.826
ATOM 83 C ASN 5 10.465 17.045 10.810
ATOM 84 O ASN 5 9.859 18.029 11.237
ATOM 85 N CYS 6 11.425 16.451 11.535
ATOM 86 H CYS 6 11.828 15.580 11.218
ATOM 87 CA CYS 6 11.826 16.949 12.857
ATOM 88 HA CYS 6 10.972 16.764 13.509
ATOM 89 CB CYS 6 13.027 16.166 13.400
ATOM 90 2HB CYS 6 13.865 16.235 12.706
ATOM 91 3HB CYS 6 13.333 16.638 14.333
ATOM 92 SG CYS 6 12.749 14.431 13.781
ATOM 93 C CYS 6 12.168 18.461 12.878
ATOM 94 O CYS 6 12.988 18.907 12.066
ATOM 95 N PRO 7 11.599 19.242 13.821
ATOM 96 CD PRO 7 10.713 18.793 14.890
ATOM 97 2HD PRO 7 11.226 18.043 15.492
ATOM 98 3HD PRO 7 9.791 18.364 14.495
ATOM 99 CG PRO 7 10.384 20.021 15.738
ATOM 100 2HG PRO 7 11.008 20.005 16.632
ATOM 101 3HG PRO 7 9.330 20.057 16.013
ATOM 102 CB PRO 7 10.737 21.209 14.844
ATOM 103 2HB PRO 7 11.090 22.059 15.428
ATOM 104 3HB PRO 7 9.867 21.503 14.258
ATOM 105 CA PRO 7 11.826 20.682 13.912
ATOM 106 HA PRO 7 11.713 21.122 12.921
ATOM 107 C PRO 7 13.205 21.036 14.481
ATOM 108 O PRO 7 13.546 20.629 15.598
ATOM 109 N LEU 8 13.960 21.851 13.738
ATOM 110 H LEU 8 13.510 22.266 12.935
ATOM 111 CA LEU 8 15.305 22.362 14.034
ATOM 112 HA LEU 8 15.625 22.903 13.144
ATOM 113 CB LEU 8 15.193 23.416 15.158
ATOM 114 2HB LEU 8 15.023 22.909 16.108
ATOM 115 3HB LEU 8 16.147 23.939 15.224
ATOM 116 CG LEU 8 14.077 24.471 14.980
ATOM 117 HG LEU 8 13.107 23.989 14.862
ATOM 118 CD1 LEU 8 13.977 25.302 16.253
ATOM 119 1HD1 LEU 8 13.282 24.804 16.929
ATOM 120 2HD1 LEU 8 14.951 25.381 16.736
ATOM 121 3HD1 LEU 8 13.591 26.297 16.028
ATOM 122 CD2 LEU 8 14.334 25.370 13.766
ATOM 123 1HD2 LEU 8 15.281 25.899 13.873
ATOM 124 2HD2 LEU 8 14.358 24.775 12.853
ATOM 125 3HD2 LEU 8 13.531 26.101 13.676
ATOM 126 C LEU 8 16.436 21.320 14.278
ATOM 127 O LEU 8 17.529 21.506 13.739
ATOM 128 N GLY 9 16.215 20.229 15.022
ATOM 129 H GLY 9 15.289 20.119 15.411
ATOM 130 CA GLY 9 17.232 19.220 15.378
ATOM 131 2HA GLY 9 17.600 18.714 14.486
ATOM 132 3HA GLY 9 18.074 19.715 15.861
ATOM 133 C GLY 9 16.726 18.193 16.374
ATOM 134 O GLY 9 16.916 18.469 17.576
ATOM 135 OXT GLY 9 16.117 17.176 15.962
ATOM 136 X GLY 9 15.802 16.559 18.116 +1.00
END
Check the model structure
You should check the model structure by using viewing software such as “PyMol” and “Chimera”. The current model has a disulfide bond between “CYC1” and “CYC6”.
Convert PDB file to Bridge format file
$ ${PDF_HOME}/bin/pdb2brd.py 1NPO_model.pdb 1NPO_model.brd
Note
You can check the bridge file contents using the following utility.
$ ${PDF_HOME}/bin/brd2txt.py 1NPO_model.brd
Create input file for QCLObot
You save the following text as 1NPO_model.QCLO.yaml .
---
tasks:
- name: default
brd_file: 1NPO.model.brd
basis_set: DZVP2
guess: Harris
XC_functional: B3LYP
J_engine: CD
K_engine: CD
XC_engine: grid
# ----------------------------------------------------------------------
# STEP 1
# ----------------------------------------------------------------------
# The res_1 bounds to the res_6 by the dislufide bond.
- name: res_1_res_6
sp: true
fragments:
- name: res_1-1
brd_select: /model_1/A/1/
- name: NME_1
add_NME: true
brd_select: /model_1/A/2/
- name: ACE_6
add_ACE: true
brd_select: /model_1/A/5/
- name: res_6-6
brd_select: /model_1/A/6/
- name: NME_6
add_NME: true
brd_select: /model_1/A/7/
- name: res_2-2
sp: true
fragments:
- name: ACE_2
add_ACE: true
brd_select: /model_1/A/1/
- name: res_2-2
brd_select: /model_1/A/2/
- name: NME_2
add_NME: true
brd_select: /model_1/A/3/
- name: res_3-3
sp: true
fragments:
- name: ACE_3
add_ACE: true
brd_select: /model_1/A/2/
- name: res_3-3
brd_select: /model_1/A/3/
- name: NME_3
add_NME: true
brd_select: /model_1/A/4/
- name: res_4-4
sp: true
fragments:
- name: ACE_4
add_ACE: true
brd_select: /model_1/A/3/
- name: res_4-4
brd_select: /model_1/A/4/
- name: NME_4
add_NME: true
brd_select: /model_1/A/5/
- name: res_5-5
sp: true
fragments:
- name: ACE_5
add_ACE: true
brd_select: /model_1/A/4/
- name: res_5-5
brd_select: /model_1/A/5/
- name: NME_5
add_NME: true
brd_select: /model_1/A/6/
- name: res_7-7
sp: true
fragments:
- name: ACE_7
add_ACE: true
brd_select: /model_1/A/6/
- name: res_7-7
brd_select: /model_1/A/7/
- name: NME_7
add_NME: true
brd_select: /model_1/A/8/
- name: res_8-8
sp: true
fragments:
- name: ACE_8
add_ACE: true
brd_select: /model_1/A/7/
- name: res_8-8
brd_select: /model_1/A/8/
- name: NME_8
add_NME: true
brd_select: /model_1/A/9/
- name: res_9-9
sp: true
fragments:
- name: ACE_9
add_ACE: true
brd_select: /model_1/A/8/
- name: res_9-9
brd_select: /model_1/A/9/
# ----------------------------------------------------------------------
# STEP 2
# ----------------------------------------------------------------------
- name: res_1-7
guess: QCLO
sp: true
fragments:
- name: res_1-6
fragments:
- name: res_1-1
reference:
frame: res_1_res_6
fragment: res_1-1
- name: res_2-2
reference:
frame: res_2-2
fragment: res_2-2
- name: res_3-3
reference:
frame: res_3-3
fragment: res_3-3
- name: res_4-4
reference:
frame: res_4-4
fragment: res_4-4
- name: res_5-5
reference:
frame: res_5-5
fragment: res_5-5
- name: res_6-6
reference:
frame: res_1_res_6
fragment: res_6-6
- name: res_7-7
fragments:
- name: res_7-7
reference:
frame: res_7-7
fragment: res_7-7
- name: NME_7
reference:
frame: res_7-7
fragment: NME_7
- name: res_6-9
guess: QCLO
sp: true
fragments:
- name: res_1_res_6
fragments:
- name: res_1-1
reference:
frame: res_1_res_6
fragment: res_1-1
- name: NME_1
reference:
frame: res_1_res_6
fragment: NME_1
- name: ACE_6
reference:
frame: res_1_res_6
fragment: ACE_6
- name: res_6-6
reference:
frame: res_1_res_6
fragment: res_6-6
- name: res_7-9
fragments:
- name: res_7-7
reference:
frame: res_7-7
fragment: res_7-7
- name: res_8-8
reference:
frame: res_8-8
fragment: res_8-8
- name: res_9-9
reference:
frame: res_9-9
fragment: res_9-9
# ----------------------------------------------------------------------
# STEP 3
# ----------------------------------------------------------------------
- name: res_1-9
guess: QCLO
sp: true
fragments:
- name: res_1-9
fragments:
- name: res_1-6
reference:
frame: res_1-7
fragment: res_1-6
- name: res_7-9
reference:
frame: res_6-9
fragment: res_7-9
Run QCLObot
$ ${PDF_HOME}/bin/QCLObot.py 1NPO_mode.QCLO.yaml