Setting up calculation model

Prepare Oxytocin model

You can get Oxytocin model (1NPO_model.pdb) 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 dislufide 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