From NWChem
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Threads 11
Posts 37
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| 2:19:23 AM PDT - Mon, Jun 9th 2014 |
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Hello,
I tried to compute a QMMM calculation from a pdb file. First of all, I want to create the topology and restart file using the prepare module. I read the documentation about the preparation of this file but I do not understand what im doing wrong...
Here is my PDB file :
ATOM 1 1C0 RE1 1 8.779 4.095 0.000 1.00 0.00 C
ATOM 3 1C2 RE1 1 2.925 0.000 0.000 1.00 0.00 C
ATOM 4 1C3 RE1 1 2.925 8.189 0.000 1.00 0.00 C
ATOM 5 1C4 RE1 1 2.925 0.000 8.184 1.00 0.00 C
ATOM 6 1C5 RE1 1 2.925 8.189 8.184 1.00 0.00 C
...
ATOM 2 1C1 RE2 2 8.779 4.095 8.184 1.00 0.00 C
ATOM 19 1H0 RE2 2 9.378 4.746 7.641 1.00 0.00 H
ATOM 39 3H0 RE2 2 8.179 3.552 7.533 1.00 0.00 H
ATOM 105 8H4 RE2 2 9.378 3.443 8.727 1.00 0.00 H
ATOM 106 8H5 RE2 2 8.179 4.638 8.836 1.00 0.00 H
My input file is :
title "QMMM cell"
echo
start qmmm_cell
prepare
source cell1.pdb
new_top new_seq
new_rst
#define quantum region residue:name
#modify atom 2:1C1 quantum
#modify atom 2:1H0 quantum
#modify atom 2:3H0 quantum
#modify atom 2:8H4 quantum
#modify atom 2:8H5 quantum
modify segment 2 quantum
update lists
ignore
write cell.rst
write qmmm.pdb
end
Unfortunetly, the qmmm.pdb file does not want to be created and I have this output file:
...
Coordinates missing for atom 1:RE1 H7
Coordinates missing for atom 1:RE1 H8
Coordinates missing for atom 1:RE1 H9
Coordinates missing for atom 1:RE1 H0
Coordinates missing for atom 1:RE1 H1
Coordinates missing for atom 1:RE1 H6
Coordinates missing for atom 1:RE1 H7
Coordinates missing for atom 1:RE1 H8
Coordinates missing for atom 1:RE1 H5
Coordinates missing for atom 1:RE1 H6
Coordinates missing for atom 1:RE1 H7
Added counterion with energy 0.000 kJ/mol
Grid specifications for non-bonded atoms done
**********
* 0: pre_misfit: missing non hydrogen coordinates 9999
You can remark that I fixed 2 different residual name. The first one is the MM region and the second is the QM region that I want to define in the prepare module.
When I define the QM region atom per atom with the commented command, I obtain another output :
modify atom 2:1C1 set 0 quantum
**********
* 0: Atom not found for quantum 0
What I am doing wrong? How can I define QM and MM region in the input file?
Thank you in advance!
Guillaume
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Threads 5
Posts 19
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| 4:22:23 AM PDT - Tue, Jun 10th 2014 |
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Hi Guillaume,
I tried to use your input and your geometry and it works for me. Are you sure that there are no typo errors in the file names or similar stuffs?
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Threads 11
Posts 37
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| 4:55:21 AM PDT - Tue, Jun 10th 2014 |
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Hi Varnon,
I checked again my pdb file and the name and there are no typo Errors. The only difference is that I have some negative coordinates like this :
ATOM 141 H21 RE1 1 9.378 8.841 4.635 1.00 0.00 H
ATOM 142 H22 RE1 1 8.179 8.732 3.441 1.00 0.00 H
ATOM 143 H23 RE1 1 -0.852 6.433 1.492 1.00 0.00 H
ATOM 144 H24 RE1 1 12.560 6.433 1.492 1.00 0.00 H
ATOM 145 H25 RE1 1 -0.852 5.851 5.584 1.00 0.00 H
ATOM 146 H26 RE1 1 12.560 5.851 5.584 1.00 0.00 H
ATOM 147 H27 RE1 1 -0.852 1.757 6.692 1.00 0.00 H
ATOM 148 H28 RE1 1 12.560 1.757 6.692 1.00 0.00 H
ATOM 149 H29 RE1 1 -0.852 2.338 2.600 1.00 0.00 H
ATOM 150 H30 RE1 1 12.560 2.338 2.600 1.00 0.00 H
Is it Possible that i would be due to the space between the x coordinate and the number of segment?
Thank you a lot!
Guillaume
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Clicked A Few Times
Threads 11
Posts 37
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| 4:55:35 AM PDT - Tue, Jun 10th 2014 |
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Hi Varnon,
I checked again my pdb file and the name and there are no typo Errors. The only difference is that I have some negative coordinates like this :
ATOM 141 H21 RE1 1 9.378 8.841 4.635 1.00 0.00 H
ATOM 142 H22 RE1 1 8.179 8.732 3.441 1.00 0.00 H
ATOM 143 H23 RE1 1 -0.852 6.433 1.492 1.00 0.00 H
ATOM 144 H24 RE1 1 12.560 6.433 1.492 1.00 0.00 H
ATOM 145 H25 RE1 1 -0.852 5.851 5.584 1.00 0.00 H
ATOM 146 H26 RE1 1 12.560 5.851 5.584 1.00 0.00 H
ATOM 147 H27 RE1 1 -0.852 1.757 6.692 1.00 0.00 H
ATOM 148 H28 RE1 1 12.560 1.757 6.692 1.00 0.00 H
ATOM 149 H29 RE1 1 -0.852 2.338 2.600 1.00 0.00 H
ATOM 150 H30 RE1 1 12.560 2.338 2.600 1.00 0.00 H
Is it Possible that it could be due to the space between the x coordinate and the number of segment?
Thank you a lot!
Guillaume
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Edited On 5:03:12 AM PDT - Tue, Jun 10th 2014 by Guillaume
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Threads 5
Posts 19
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| 8:40:58 AM PDT - Tue, Jun 10th 2014 |
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Yes,
the position of the columns are fixed. Check here how to do a proper PDB
http://www.nwchem-sw.org/index.php/QMMM_Appendix
and here an example of PDB with the proper format www.nwchem-sw.org/images/N3o3.pdb
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Threads 11
Posts 37
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| 12:35:26 PM PDT - Tue, Jun 10th 2014 |
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test
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Edited On 2:55:55 AM PDT - Wed, Jun 11th 2014 by Guillaume
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Threads 11
Posts 37
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| 5:29:00 AM PDT - Wed, Jun 11th 2014 |
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Back again!
I changed my PDB file to correspond exactly with the documentation and the PDB with proper format.
Every column are at the same position and have the same number of space...
To be sure, I give you the PDB file above this post
I tested this input and my new output file gave me this lign :
PGFIO-F-231/formatted read/internal file/error on data conversion.
In source file pre_pdbseq.F, at line number 189
I found this post : http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id1165/Fortran_runtime_error%3A_Bad...
It means that I have a wrong PDB file but I do not understand where the error could be there...
Thank you so much to help me!
Guillaume
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Threads 11
Posts 37
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| 5:31:45 AM PDT - Wed, Jun 11th 2014 |
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ATOM 1 1C0 RE1 1 8.779 4.095 0.000 1.00 0.00 C
ATOM 2 1C1 RE2 2 8.779 4.095 8.184 1.00 0.00 C
ATOM 3 1C2 RE1 1 2.925 0.000 0.000 1.00 0.00 C
ATOM 4 1C3 RE1 1 2.925 8.189 0.000 1.00 0.00 C
ATOM 5 1C4 RE1 1 2.925 0.000 8.184 1.00 0.00 C
ATOM 6 1C5 RE1 1 2.925 8.189 8.184 1.00 0.00 C
ATOM 7 1C6 RE1 1 2.929 0.000 4.092 1.00 0.00 C
ATOM 8 1C7 RE1 1 2.929 8.189 4.092 1.00 0.00 C
ATOM 9 1C8 RE1 1 8.783 4.095 4.092 1.00 0.00 C
ATOM 10 1C9 RE1 1 2.929 4.095 0.000 1.00 0.00 C
ATOM 11 2C0 RE1 1 2.929 4.095 8.184 1.00 0.00 C
ATOM 12 2C1 RE1 1 8.783 0.000 0.000 1.00 0.00 C
ATOM 13 2C2 RE1 1 8.783 8.189 0.000 1.00 0.00 C
ATOM 14 2C3 RE1 1 8.783 0.000 8.184 1.00 0.00 C
ATOM 15 2C4 RE1 1 8.783 8.189 8.184 1.00 0.00 C
ATOM 16 2C5 RE1 1 8.779 0.000 4.092 1.00 0.00 C
ATOM 17 2C6 RE1 1 8.779 8.189 4.092 1.00 0.00 C
ATOM 18 2C7 RE1 1 2.925 4.095 4.092 1.00 0.00 C
ATOM 19 1H0 RE2 2 9.378 4.746 7.641 1.00 0.00 H
ATOM 20 1H1 RE1 1 3.524 0.651 7.641 1.00 0.00 H
ATOM 21 1H2 RE1 1 2.330 7.538 3.549 1.00 0.00 H
ATOM 22 1H3 RE1 1 8.183 3.443 3.549 1.00 0.00 H
ATOM 23 1H4 RE1 1 9.378 3.443 0.543 1.00 0.00 H
ATOM 24 1H5 RE1 1 3.524 7.538 0.543 1.00 0.00 H
ATOM 25 1H6 RE1 1 2.330 0.651 4.635 1.00 0.00 H
ATOM 26 1H7 RE1 1 8.183 4.746 4.635 1.00 0.00 H
ATOM 27 1H8 RE1 1 2.330 3.443 0.543 1.00 0.00 H
ATOM 28 1H9 RE1 1 8.183 7.538 0.543 1.00 0.00 H
ATOM 29 2H0 RE1 1 9.378 0.651 4.635 1.00 0.00 H
ATOM 30 2H1 RE1 1 3.524 4.746 4.635 1.00 0.00 H
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Threads 11
Posts 37
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| 5:33:50 AM PDT - Wed, Jun 11th 2014 |
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ATOM 31 2H2 RE1 1 2.330 4.746 7.641 1.00 0.00 H
ATOM 32 2H3 RE1 1 8.183 0.651 7.641 1.00 0.00 H
ATOM 33 2H4 RE1 1 9.378 7.538 3.549 1.00 0.00 H
ATOM 34 2H5 RE1 1 3.524 3.443 3.549 1.00 0.00 H
ATOM 35 2H6 RE1 1 8.179 4.638 0.651 1.00 0.00 H
ATOM 36 2H7 RE1 1 2.325 0.543 0.651 1.00 0.00 H
ATOM 37 2H8 RE1 1 3.529 7.646 4.744 1.00 0.00 H
ATOM 38 2H9 RE1 1 9.383 3.552 4.744 1.00 0.00 H
ATOM 39 3H0 RE2 2 8.179 3.552 7.533 1.00 0.00 H
ATOM 40 3H1 RE1 1 2.325 7.646 7.533 1.00 0.00 H
ATOM 41 3H2 RE1 1 3.529 0.543 3.441 1.00 0.00 H
ATOM 42 3H3 RE1 1 9.383 4.638 3.441 1.00 0.00 H
ATOM 43 3H4 RE1 1 3.529 3.552 7.533 1.00 0.00 H
ATOM 44 3H5 RE1 1 9.383 7.646 7.533 1.00 0.00 H
ATOM 45 3H6 RE1 1 8.179 0.543 3.441 1.00 0.00 H
ATOM 46 3H7 RE1 1 2.325 4.638 3.441 1.00 0.00 H
ATOM 47 3H8 RE1 1 3.529 4.638 0.651 1.00 0.00 H
ATOM 48 3H9 RE1 1 9.383 0.543 0.651 1.00 0.00 H
ATOM 49 4H0 RE1 1 8.179 7.646 4.744 1.00 0.00 H
ATOM 50 4H1 RE1 1 2.325 3.552 4.744 1.00 0.00 H
ATOM 51 2C8 RE1 1 0.000 5.975 1.885 1.00 0.00 C
ATOM 52 2C9 RE1 1 11.708 5.975 1.885 1.00 0.00 C
ATOM 53 3C0 RE1 1 5.854 1.880 1.885 1.00 0.00 C
ATOM 54 3C1 RE1 1 0.000 6.309 5.977 1.00 0.00 C
ATOM 55 3C2 RE1 1 11.708 6.309 5.977 1.00 0.00 C
ATOM 56 3C3 RE1 1 5.854 2.214 5.977 1.00 0.00 C
ATOM 57 3C4 RE1 1 0.000 2.214 6.299 1.00 0.00 C
ATOM 58 3C5 RE1 1 11.708 2.214 6.299 1.00 0.00 C
ATOM 59 3C6 RE1 1 5.854 6.309 6.299 1.00 0.00 C
ATOM 60 3C7 RE1 1 0.000 1.880 2.207 1.00 0.00 C
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Threads 11
Posts 37
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| 5:34:52 AM PDT - Wed, Jun 11th 2014 |
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ATOM 61 3C8 RE1 1 11.708 1.880 2.207 1.00 0.00 C
ATOM 62 3C9 RE1 1 5.854 5.975 2.207 1.00 0.00 C
ATOM 63 4H2 RE1 1 0.000 4.962 1.631 1.00 0.00 H
ATOM 64 4H3 RE1 1 11.708 4.962 1.631 1.00 0.00 H
ATOM 65 4H4 RE1 1 5.854 0.867 1.631 1.00 0.00 H
ATOM 66 4H5 RE1 1 0.000 7.322 5.723 1.00 0.00 H
ATOM 67 4H6 RE1 1 11.708 7.322 5.723 1.00 0.00 H
ATOM 68 4H7 RE1 1 5.854 3.227 5.723 1.00 0.00 H
ATOM 69 4H8 RE1 1 0.000 3.227 6.554 1.00 0.00 H
ATOM 70 4H9 RE1 1 11.708 3.227 6.554 1.00 0.00 H
ATOM 71 5H0 RE1 1 5.854 7.322 6.554 1.00 0.00 H
ATOM 72 5H1 RE1 1 0.000 0.867 2.461 1.00 0.00 H
ATOM 73 5H2 RE1 1 11.708 0.867 2.461 1.00 0.00 H
ATOM 74 5H3 RE1 1 5.854 4.962 2.461 1.00 0.00 H
ATOM 75 5H4 RE1 1 0.000 6.073 2.925 1.00 0.00 H
ATOM 76 5H5 RE1 1 11.708 6.073 2.925 1.00 0.00 H
ATOM 77 5H6 RE1 1 5.854 1.979 2.925 1.00 0.00 H
ATOM 78 5H7 RE1 1 0.000 6.211 7.017 1.00 0.00 H
ATOM 79 5H8 RE1 1 11.708 6.211 7.017 1.00 0.00 H
ATOM 80 5H9 RE1 1 5.854 2.116 7.017 1.00 0.00 H
ATOM 81 6H0 RE1 1 0.000 2.116 5.259 1.00 0.00 H
ATOM 82 6H1 RE1 1 11.708 2.116 5.259 1.00 0.00 H
ATOM 83 6H2 RE1 1 5.854 6.211 5.259 1.00 0.00 H
ATOM 84 6H3 RE1 1 0.000 1.979 1.167 1.00 0.00 H
ATOM 85 6H4 RE1 1 11.708 1.979 1.167 1.00 0.00 H
ATOM 86 6H5 RE1 1 5.854 6.073 1.167 1.00 0.00 H
ATOM 87 6H6 RE1 1 0.852 6.433 1.492 1.00 0.00 H
ATOM 88 6H7 RE1 1 6.706 2.338 1.492 1.00 0.00 H
ATOM 89 6H8 RE1 1 10.856 5.851 5.584 1.00 0.00 H
ATOM 90 6H9 RE1 1 5.002 1.757 5.584 1.00 0.00 H
ATOM 91 7H0 RE1 1 0.852 1.757 6.692 1.00 0.00 H
ATOM 92 7H1 RE1 1 6.706 5.851 6.692 1.00 0.00 H
ATOM 93 7H2 RE1 1 10.856 2.338 2.600 1.00 0.00 H
ATOM 94 7H3 RE1 1 5.002 6.433 2.600 1.00 0.00 H
ATOM 95 7H4 RE1 1 10.856 1.757 6.692 1.00 0.00 H
ATOM 96 7H5 RE1 1 5.002 5.851 6.692 1.00 0.00 H
ATOM 97 7H6 RE1 1 0.852 2.338 2.600 1.00 0.00 H
ATOM 98 7H7 RE1 1 6.706 6.433 2.600 1.00 0.00 H
ATOM 99 7H8 RE1 1 10.856 6.433 1.492 1.00 0.00 H
ATOM 100 7H9 RE1 1 5.002 2.338 1.492 1.00 0.00 H
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Threads 11
Posts 37
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| 5:35:51 AM PDT - Wed, Jun 11th 2014 |
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ATOM 101 8H0 RE1 1 0.852 5.851 5.584 1.00 0.00 H
ATOM 102 8H1 RE1 1 6.706 1.757 5.584 1.00 0.00 H
ATOM 103 8H2 RE1 1 9.378 4.746 -0.543 1.00 0.00 H
ATOM 104 8H3 RE1 1 8.179 3.552 -0.651 1.00 0.00 H
ATOM 105 8H4 RE2 2 9.378 3.443 8.727 1.00 0.00 H
ATOM 106 8H5 RE2 2 8.179 4.638 8.836 1.00 0.00 H
ATOM 107 8H6 RE1 1 3.524 0.651 -0.543 1.00 0.00 H
ATOM 108 8H7 RE1 1 3.524 -0.651 0.543 1.00 0.00 H
ATOM 109 8H8 RE1 1 2.325 -0.543 -0.651 1.00 0.00 H
ATOM 110 8H9 RE1 1 3.524 8.841 -0.543 1.00 0.00 H
ATOM 111 9H0 RE1 1 2.325 8.732 0.651 1.00 0.00 H
ATOM 112 9H1 RE1 1 2.325 7.646 -0.651 1.00 0.00 H
ATOM 113 9H2 RE1 1 3.524 -0.651 8.727 1.00 0.00 H
ATOM 114 9H3 RE1 1 2.325 0.543 8.836 1.00 0.00 H
ATOM 115 9H4 RE1 1 2.325 -0.543 7.533 1.00 0.00 H
ATOM 116 9H5 RE1 1 3.524 8.841 7.641 1.00 0.00 H
ATOM 117 9H6 RE1 1 3.524 7.538 8.727 1.00 0.00 H
ATOM 118 9H7 RE1 1 2.325 8.732 8.836 1.00 0.00 H
ATOM 119 9H8 RE1 1 2.330 -0.651 3.549 1.00 0.00 H
ATOM 120 9H9 RE1 1 3.529 -0.543 4.744 1.00 0.00 H
ATOM 121 H01 RE1 1 2.330 8.841 4.635 1.00 0.00 H
ATOM 122 H02 RE1 1 3.529 8.732 3.441 1.00 0.00 H
ATOM 123 H03 RE1 1 2.330 4.746 -0.543 1.00 0.00 H
ATOM 124 H04 RE1 1 3.529 3.552 -0.651 1.00 0.00 H
ATOM 125 H05 RE1 1 2.330 3.443 8.727 1.00 0.00 H
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Threads 11
Posts 37
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| 5:36:39 AM PDT - Wed, Jun 11th 2014 |
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ATOM 126 H06 RE1 1 8.183 -0.651 0.543 1.00 0.00 H
ATOM 128 H08 RE1 1 8.183 0.651 -0.543 1.00 0.00 H
ATOM 129 H09 RE1 1 9.383 -0.543 -0.651 1.00 0.00 H
ATOM 130 H10 RE1 1 8.183 8.841 -0.543 1.00 0.00 H
ATOM 131 H11 RE1 1 9.383 7.646 -0.651 1.00 0.00 H
ATOM 132 H12 RE1 1 9.383 8.732 0.651 1.00 0.00 H
ATOM 133 H13 RE1 1 8.183 -0.651 8.727 1.00 0.00 H
ATOM 134 H14 RE1 1 9.383 -0.543 7.533 1.00 0.00 H
ATOM 135 H15 RE1 1 9.383 0.543 8.836 1.00 0.00 H
ATOM 136 H16 RE1 1 8.183 7.538 8.727 1.00 0.00 H
ATOM 137 H17 RE1 1 8.183 8.841 7.641 1.00 0.00 H
ATOM 138 H18 RE1 1 9.383 8.732 8.836 1.00 0.00 H
ATOM 139 H19 RE1 1 9.378 -0.651 3.549 1.00 0.00 H
ATOM 140 H20 RE1 1 8.179 -0.543 4.744 1.00 0.00 H
ATOM 141 H21 RE1 1 9.378 8.841 4.635 1.00 0.00 H
ATOM 142 H22 RE1 1 8.179 8.732 3.441 1.00 0.00 H
ATOM 143 H23 RE1 1 -0.852 6.433 1.492 1.00 0.00 H
ATOM 144 H24 RE1 1 12.560 6.433 1.492 1.00 0.00 H
ATOM 145 H25 RE1 1 -0.852 5.851 5.584 1.00 0.00 H
ATOM 146 H26 RE1 1 12.560 5.851 5.584 1.00 0.00 H
ATOM 147 H27 RE1 1 -0.852 1.757 6.692 1.00 0.00 H
ATOM 148 H28 RE1 1 12.560 1.757 6.692 1.00 0.00 H
ATOM 149 H29 RE1 1 -0.852 2.338 2.600 1.00 0.00 H
ATOM 150 H30 RE1 1 12.560 2.338 2.600 1.00 0.00 H
END
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Threads 11
Posts 37
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| 5:39:15 AM PDT - Wed, Jun 11th 2014 |
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| I am really sorry but I did not succeed to send te PDB in one block...
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Threads 5
Posts 19
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| 2:51:06 AM PDT - Thu, Jun 12th 2014 |
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Hi,
ok, I think the problem is the column 5, in which the numbers have to be consecutive and if you repeat a fragment as to be the same of the first but with a different number like:
RE1 1
RE1 1
RE1 1
RE2 2
RE2 2
RE2 2
XXX 3
XXX 3
XXX 3
RE1 4
RE1 4
RE1 4
so, I would suggest you to use the same fragment (and number in the 5^ column) for all the molecule and to define the quantum region by atom by atom keyword, or to shift all your quantum atoms at the end (or start) of your pdb, and to use the segment keyword avoiding situation like:
RE1 1
RE2 2
RE1 1
Ale
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Threads 11
Posts 37
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| 12:32:38 AM PDT - Fri, Jun 13th 2014 |
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Hi,
I changed my PDB file and it was due to this problem. Now I have just the error due to the fragment file described in the QMMM appendix!
Problem Resolved! 
thank you!
Guillaume
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