QMMM missing coordinates problem

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Dear All

When I run the QMMM calculation. The output file shows the error message as below. Does anyone know how to solve this? or what is the problem? Thanks a lot.

I also give my input and structure pdb files in the google drive link
(https://drive.google.com/drive/folders/1O-7I0NUDRGSbDy10DkTDP3KLT7f4X0Ji?usp=sharing)


Error message --------------------------------------------

db_size nwchm_form.pdb
PDB OPEN  nwchm_form.pdb
number of segments read from ATOM cards
PDB file nwchm_form.pdb
Number of atoms 130
Number of segments 5
Number of SS-bonds 0
Number of solvent molecules 0


pdb_read nwchm_form.pdb
PDB OPEN  nwchm_form.pdb
ATOM C MOA 1 4.208 8.896 1.198
ATOM H MOA 1 3.457 8.212 0.790
ATOM H MOA 1 3.702 9.561 1.908
ATOM H MOA 1 4.580 9.509 0.375
ATOM C MOA 1 5.305 8.098 1.904
ATOM C MOA 1 4.669 7.316 3.048
ATOM H MOA 1 4.200 8.005 3.759
ATOM H MOA 1 3.880 6.661 2.664
ATOM H MOA 1 5.385 6.706 3.597
ATOM C MOA 1 6.581 8.966 2.191
ATOM H MOA 1 6.437 10.009 2.494
ATOM C MOA 1 7.022 8.660 0.734
ATOM H MOA 1 6.586 9.336 -0.003
ATOM H MOA 1 8.098 8.578 0.568
ATOM C MOA 1 6.221 7.342 0.885
ATOM H MOA 1 5.742 6.924 -0.006
ATOM C MOA 1 7.097 6.308 1.601
ATOM H MOA 1 7.863 5.927 0.919
ATOM H MOA 1 6.501 5.437 1.911
ATOM C MOA 1 7.772 6.931 2.800
ATOM H MOA 1 8.439 6.321 3.405
ATOM C MOA 1 7.533 8.215 3.102
ATOM C MOA 1 8.187 8.944 4.233
ATOM H MOA 1 7.441 9.413 4.884
ATOM H MOA 1 8.813 8.279 4.834
ATOM H MOA 1 8.821 9.756 3.850
ATOM C MOA 2 6.556 3.365 3.039
ATOM H MOA 2 7.308 3.533 2.262
ATOM H MOA 2 6.400 4.315 3.563
ATOM H MOA 2 6.972 2.655 3.756
ATOM C MOA 2 5.251 2.888 2.401
ATOM C MOA 2 4.755 3.975 1.453
ATOM H MOA 2 4.576 4.903 2.007
ATOM H MOA 2 5.516 4.191 0.697
ATOM H MOA 2 3.830 3.706 0.944
ATOM C MOA 2 4.257 2.286 3.457
ATOM H MOA 2 4.196 2.768 4.438
ATOM C MOA 2 5.042 0.953 3.319
ATOM H MOA 2 5.928 0.903 3.953
ATOM H MOA 2 4.454 0.040 3.434
ATOM C MOA 2 5.363 1.418 1.877
ATOM H MOA 2 6.318 1.113 1.437
ATOM C MOA 2 4.179 1.070 0.967
ATOM H MOA 2 4.163 -0.005 0.766
ATOM H MOA 2 4.278 1.565 -0.010
ATOM C MOA 2 2.879 1.467 1.624
ATOM H MOA 2 1.944 1.272 1.102
ATOM C MOA 2 2.897 2.058 2.826
ATOM C MOA 2 1.667 2.444 3.588
ATOM H MOA 2 1.700 3.499 3.881
ATOM H MOA 2 0.759 2.267 3.005
ATOM H MOA 2 1.595 1.864 4.518
ATOM C MOA 3 8.669 7.772 8.812
ATOM H MOA 3 7.930 8.564 8.968
ATOM H MOA 3 9.030 7.456 9.799
ATOM H MOA 3 9.513 8.206 8.274
ATOM C MOA 3 8.021 6.597 8.080
ATOM C MOA 3 6.886 6.059 8.945
ATOM H MOA 3 7.278 5.719 9.910
ATOM H MOA 3 6.161 6.852 9.151
ATOM H MOA 3 6.360 5.223 8.485
ATOM C MOA 3 9.084 5.594 7.507
ATOM H MOA 3 9.974 5.387 8.111
ATOM C MOA 3 9.207 6.544 6.285
ATOM H MOA 3 9.902 7.369 6.445
ATOM H MOA 3 9.419 6.064 5.327
ATOM C MOA 3 7.736 6.933 6.579
ATOM H MOA 3 7.417 7.953 6.345
ATOM C MOA 3 6.810 5.886 5.950
ATOM H MOA 3 6.775 6.019 4.864
ATOM H MOA 3 5.778 6.010 6.309
ATOM C MOA 3 7.306 4.494 6.259
ATOM H MOA 3 6.756 3.640 5.868
ATOM C MOA 3 8.403 4.333 7.012
ATOM C MOA 3 9.008 3.002 7.335
ATOM H MOA 3 9.138 2.881 8.416
ATOM H MOA 3 8.398 2.178 6.957
ATOM H MOA 3 10.009 2.918 6.889
ATOM C MOA 4 2.950 6.921 8.834
ATOM H MOA 4 3.621 7.232 9.640
ATOM H MOA 4 1.930 6.903 9.238
ATOM H MOA 4 3.215 5.899 8.557
ATOM C MOA 4 3.044 7.908 7.671
ATOM C MOA 4 2.617 9.283 8.172
ATOM H MOA 4 1.586 9.245 8.539
ATOM H MOA 4 3.249 9.591 9.012
ATOM H MOA 4 2.670 10.052 7.403
ATOM C MOA 4 2.399 7.342 6.356
ATOM H MOA 4 1.482 6.751 6.446
ATOM C MOA 4 3.746 6.611 6.103
ATOM H MOA 4 3.822 5.651 6.616
ATOM H MOA 4 4.036 6.493 5.057
ATOM C MOA 4 4.398 7.769 6.899
ATOM H MOA 4 5.292 7.549 7.490
ATOM C MOA 4 4.615 8.959 5.956
ATOM H MOA 4 5.457 8.759 5.286
ATOM H MOA 4 4.880 9.863 6.523
ATOM C MOA 4 3.376 9.206 5.130
ATOM H MOA 4 3.381 10.015 4.402
ATOM C MOA 4 2.294 8.436 5.310
ATOM C MOA 4 1.035 8.560 4.510
ATOM H MOA 4 0.163 8.671 5.164
ATOM H MOA 4 1.074 9.411 3.825
ATOM H MOA 4 0.867 7.651 3.916
ATOM C MOA 5 1.081 4.588 7.374
ATOM H MOA 5 -0.011 4.538 7.334
ATOM H MOA 5 1.352 5.466 7.973
ATOM H MOA 5 1.443 4.755 6.358
ATOM C MOA 5 1.635 3.316 8.014
ATOM C MOA 5 1.088 3.215 9.434
ATOM H MOA 5 1.401 4.087 10.019
ATOM H MOA 5 -0.006 3.212 9.417
ATOM H MOA 5 1.426 2.322 9.958
ATOM C MOA 5 3.179 3.154 7.779
ATOM H MOA 5 3.802 4.054 7.818
ATOM C MOA 5 2.826 2.541 6.397
ATOM H MOA 5 2.668 3.289 5.618
ATOM H MOA 5 3.502 1.766 6.032
ATOM C MOA 5 1.504 2.081 7.062
ATOM H MOA 5 0.607 2.022 6.438
ATOM C MOA 5 1.759 0.774 7.822
ATOM H MOA 5 1.858 -0.057 7.118
ATOM H MOA 5 0.908 0.528 8.473
ATOM C MOA 5 3.026 0.881 8.638
ATOM H MOA 5 3.346 0.023 9.225
ATOM C MOA 5 3.724 2.024 8.631
ATOM C MOA 5 5.017 2.219 9.360
ATOM H MOA 5 4.975 3.102 10.006
ATOM H MOA 5 5.274 1.347 9.967
ATOM H MOA 5 5.836 2.392 8.648
PDB CLOSE nwchm_form.pdb
PDB file nwchm_form.pdb
Number of missing coordinates 120
Total number of atoms 130

Generating missing atom coordinates:   120    0

Z-matrix definitions done

Not found: atom 3 MOA H
Not found: atom 4 MOA H
Not found: atom 5 MOA C
Not found: atom 6 MOA C
Not found: atom 7 MOA H
Not found: atom 8 MOA H
Not found: atom 9 MOA H
Not found: atom 10 MOA C
Not found: atom 11 MOA H
Not found: atom 12 MOA C
Not found: atom 13 MOA H
Not found: atom 14 MOA H
Not found: atom 15 MOA C
Not found: atom 16 MOA H
Not found: atom 17 MOA C
Not found: atom 18 MOA H
Not found: atom 19 MOA H
Not found: atom 20 MOA C
Not found: atom 21 MOA H
Not found: atom 22 MOA C
Not found: atom 23 MOA C
Not found: atom 24 MOA H
Not found: atom 25 MOA H
Not found: atom 26 MOA H
Not found: atom 29 MOA H
Not found: atom 30 MOA H
Not found: atom 31 MOA C
Not found: atom 32 MOA C
Not found: atom 33 MOA H
Not found: atom 34 MOA H
Not found: atom 35 MOA H
Not found: atom 36 MOA C
Not found: atom 37 MOA H
Not found: atom 38 MOA C
Not found: atom 39 MOA H
Not found: atom 40 MOA H
Not found: atom 41 MOA C
Not found: atom 42 MOA H
Not found: atom 43 MOA C
Not found: atom 44 MOA H
Not found: atom 45 MOA H
Not found: atom 46 MOA C
Not found: atom 47 MOA H
Not found: atom 48 MOA C
Not found: atom 49 MOA C
Not found: atom 50 MOA H
Not found: atom 51 MOA H
Not found: atom 52 MOA H
Not found: atom 55 MOA H
Not found: atom 56 MOA H
Not found: atom 57 MOA C
Not found: atom 58 MOA C
Not found: atom 59 MOA H
Not found: atom 60 MOA H
Not found: atom 61 MOA H
Not found: atom 62 MOA C
Not found: atom 63 MOA H
Not found: atom 64 MOA C
Not found: atom 65 MOA H
Not found: atom 66 MOA H
Not found: atom 67 MOA C
Not found: atom 68 MOA H
Not found: atom 69 MOA C
Not found: atom 70 MOA H
Not found: atom 71 MOA H
Not found: atom 72 MOA C
Not found: atom 73 MOA H
Not found: atom 74 MOA C
Not found: atom 75 MOA C
Not found: atom 76 MOA H
Not found: atom 77 MOA H
Not found: atom 78 MOA H
Not found: atom 81 MOA H
Not found: atom 82 MOA H
Not found: atom 83 MOA C
Not found: atom 84 MOA C
Not found: atom 85 MOA H
Not found: atom 86 MOA H
Not found: atom 87 MOA H
Not found: atom 88 MOA C
Not found: atom 89 MOA H
Not found: atom 90 MOA C
Not found: atom 91 MOA H
Not found: atom 92 MOA H
Not found: atom 93 MOA C
Not found: atom 94 MOA H
Not found: atom 95 MOA C
Not found: atom 96 MOA H
Not found: atom 97 MOA H
Not found: atom 98 MOA C
Not found: atom 99 MOA H
Not found: atom 100 MOA C
Not found: atom 101 MOA C
Not found: atom 102 MOA H
Not found: atom 103 MOA H
Not found: atom 104 MOA H
Not found: atom 107 MOA H
Not found: atom 108 MOA H
Not found: atom 109 MOA C
Not found: atom 110 MOA C
Not found: atom 111 MOA H
Not found: atom 112 MOA H
Not found: atom 113 MOA H
Not found: atom 114 MOA C
Not found: atom 115 MOA H
Not found: atom 116 MOA C
Not found: atom 117 MOA H
Not found: atom 118 MOA H
Not found: atom 119 MOA C
Not found: atom 120 MOA H
Not found: atom 121 MOA C
Not found: atom 122 MOA H
Not found: atom 123 MOA H
Not found: atom 124 MOA C
Not found: atom 125 MOA H
Not found: atom 126 MOA C
Not found: atom 127 MOA C
Not found: atom 128 MOA H
Not found: atom 129 MOA H
Not found: atom 130 MOA H
Geometric rules definitions done

Coordinates missing for atom     1:MOA        C    
Coordinates missing for atom 1:MOA C
Coordinates missing for atom 1:MOA H
Coordinates missing for atom 1:MOA H
Coordinates missing for atom 1:MOA H
Coordinates missing for atom 1:MOA C
Coordinates missing for atom 1:MOA H
Coordinates missing for atom 1:MOA C
Coordinates missing for atom 1:MOA H
Coordinates missing for atom 1:MOA H
Coordinates missing for atom 1:MOA C
Coordinates missing for atom 1:MOA H
Coordinates missing for atom 1:MOA C
Coordinates missing for atom 1:MOA H
Coordinates missing for atom 1:MOA H
Coordinates missing for atom 1:MOA C
Coordinates missing for atom 1:MOA H
Coordinates missing for atom 1:MOA C
Coordinates missing for atom 1:MOA C
Coordinates missing for atom 1:MOA H
Coordinates missing for atom 1:MOA H
Coordinates missing for atom 1:MOA H
Setting up grid for atom 29
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 30
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 31
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 32
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 33
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 34
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 35
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 36
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 37
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 38
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 39
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 40
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 41
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 42
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 43
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 44
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 45
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 46
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 47
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 48
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 49
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 50
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 51
Added counterion with energy                 0.000 kJ/mol
Setting up grid for atom 52
Added counterion with energy                 0.000 kJ/mol
Coordinates missing for atom 3:MOA C
Coordinates missing for atom 3:MOA C
Coordinates missing for atom 3:MOA H
Coordinates missing for atom 3:MOA H
Coordinates missing for atom 3:MOA H
Coordinates missing for atom 3:MOA C
Coordinates missing for atom 3:MOA H
Coordinates missing for atom 3:MOA C
Coordinates missing for atom 3:MOA H
Coordinates missing for atom 3:MOA H
Coordinates missing for atom 3:MOA C
Coordinates missing for atom 3:MOA H
Coordinates missing for atom 3:MOA C
Coordinates missing for atom 3:MOA H
Coordinates missing for atom 3:MOA H
Coordinates missing for atom 3:MOA C
Coordinates missing for atom 3:MOA H
Coordinates missing for atom 3:MOA C
Coordinates missing for atom 3:MOA C
Coordinates missing for atom 3:MOA H
Coordinates missing for atom 3:MOA H
Coordinates missing for atom 3:MOA H
Coordinates missing for atom 4:MOA C
Coordinates missing for atom 4:MOA C
Coordinates missing for atom 4:MOA H
Coordinates missing for atom 4:MOA H
Coordinates missing for atom 4:MOA H
Coordinates missing for atom 4:MOA C
Coordinates missing for atom 4:MOA H
Coordinates missing for atom 4:MOA C
Coordinates missing for atom 4:MOA H
Coordinates missing for atom 4:MOA H
Coordinates missing for atom 4:MOA C
Coordinates missing for atom 4:MOA H
Coordinates missing for atom 4:MOA C
Coordinates missing for atom 4:MOA H
Coordinates missing for atom 4:MOA H
Coordinates missing for atom 4:MOA C
Coordinates missing for atom 4:MOA H
Coordinates missing for atom 4:MOA C
Coordinates missing for atom 4:MOA C
Coordinates missing for atom 4:MOA H
Coordinates missing for atom 4:MOA H
Coordinates missing for atom 4:MOA H
Coordinates missing for atom 5:MOA C
Coordinates missing for atom 5:MOA C
Coordinates missing for atom 5:MOA H
Coordinates missing for atom 5:MOA H
Coordinates missing for atom 5:MOA H
Coordinates missing for atom 5:MOA C
Coordinates missing for atom 5:MOA H
Coordinates missing for atom 5:MOA C
Coordinates missing for atom 5:MOA H
Coordinates missing for atom 5:MOA H
Coordinates missing for atom 5:MOA C
Coordinates missing for atom 5:MOA H
Coordinates missing for atom 5:MOA C
Coordinates missing for atom 5:MOA H
Coordinates missing for atom 5:MOA H
Coordinates missing for atom 5:MOA C
Coordinates missing for atom 5:MOA H
Coordinates missing for atom 5:MOA C
Coordinates missing for atom 5:MOA C
Coordinates missing for atom 5:MOA H
Coordinates missing for atom 5:MOA H
Coordinates missing for atom 5:MOA H
Grid specifications for non-bonded atoms done


**********
* 0: pre_misfit: missing non hydrogen coordinates 9999
**********


Error message---------------


my input file :

memory total 800 Mb

start test

scratch_dir /s/tayler

print debug

#this will generate topology file (asa.top), restart (asa_ref.rst), and pdb (asa_ref.pdb) files.
prepare
source nwchm_form.pdb
new_top new_seq
new_rst
modify segment 2 quantum
update lists
ignore
write test_ref.rst
write test_ref.pdb # Write out PDB file to check structure
end
task prepare

md
system test_ref
end

basis "ao basis"
* library "6-31G*"
end

dft
iterations 500
end

vib
animate
end

qmmm
region all
maxiter 129
ncycles 120
density espfit
end

# run energy calculation to generate wavefunction file for subsequent ESP charge generation
task qmmm dft energy


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