QM region input

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Posts 37
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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Posts 19
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
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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Threads 11
Posts 37
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
Edited On 4:03:12 AM PDT - Tue, Jun 10th 2014 by Guillaume

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Threads 5
Posts 19
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
test

Quote:Varnon Jun 10th 3:40 pm
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
Edited On 1:55:55 AM PDT - Wed, Jun 11th 2014 by Guillaume

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Threads 11
Posts 37
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
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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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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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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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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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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Posts 37
I am really sorry but I did not succeed to send te PDB in one block...

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Posts 19
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
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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