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I am trying to write an itp file for the compound 1,2-diethoxyethance (CCOCCOCC).I used tinker analyze to obtain the parameter file, f2.out, which I have attached to this post. In order to check if my procedure was right, I downloaded an itp file from LigParGen (UNL_6B2B1D.itp).

Every parameter in my topology file (topol.itp) matched with the parameters from LigParGen, except the dihedrals with hydrogen.

The formulae I used to go from the Torsional Angle Parameters in tinker were the ones given in the GROMACS page: https://manual.gromacs.org/documentation/2020-beta3/reference-manual/functions/bonded-interactions.html, equation block 33.

If I look at the torsional angle parameters for torsion #11 in f2.out:

7 2 6 9 -0.521 0/1 -2.018 180/2 1.996 0/3

So, $F_1 = -0.521, F_2 = -2.018, F_3 = 1.996, F_4 = 0$

I use the GROMACS formula: $$ c_0 = (F_2+(F_1+F_3)/2)\times4.184 = -5.358\\ c_1 = 0.5\times(-F_1+3F_3)\times 4.184 = 13.617\\ c_2 = (-F_2 + 4F_4)\times 4.184 = 8.443\\ c_3 = -2F_3\times4.184 = -16.7025\\ c_4 = -4F_4 = 0\\ c_5 = 0\\ $$ However, I look at the UNL file, I see that:

7 2 6 9 3 1.590 4.770 0.000 -6.360 -0.000 0.000

Clearly, the $c_i$ don't match. Why is this the case? Where am I going wrong? Every other torsion matches the formula given in block 33 of the gromacs manual page. I would appreciate any advice you have.

Some relevant lines from f2.out (I have added ## to show the lines I have used above):

Torsional Angle Parameters :

                 Atom Numbers           Amplitude, Phase and Periodicity

     1        3     1     2     6       0.468   0/3
     2        3     1     2     7       0.300   0/3
     3        3     1     2     8       0.300   0/3
     4        4     1     2     6       0.468   0/3
     5        4     1     2     7       0.300   0/3
     6        4     1     2     8       0.300   0/3
     7        5     1     2     6       0.468   0/3
     8        5     1     2     7       0.300   0/3
     9        5     1     2     8       0.300   0/3
    10        1     2     6     9       0.650   0/1  -0.250 180/2   0.670   0/3
    11        7     2     6     9      -0.521   0/1  -2.018 180/2   1.996   0/3 ##
    12        8     2     6     9      -0.521   0/1  -2.018 180/2   1.996   0/3
    13        2     6     9    10       0.650   0/1  -0.250 180/2   0.670   0/3
    14        2     6     9    11      -0.521   0/1  -2.018 180/2   1.996   0/3
    15        2     6     9    12      -0.521   0/1  -2.018 180/2   1.996   0/3
    16        6     9    10    13      -0.550   0/1
    17        6     9    10    14       0.468   0/3
    18        6     9    10    15       0.468   0/3
    19       11     9    10    13       0.468   0/3
    20       11     9    10    14       0.300   0/3
    21       11     9    10    15       0.300   0/3
    22       12     9    10    13       0.468   0/3
    23       12     9    10    14       0.300   0/3
    24       12     9    10    15       0.300   0/3
    25        9    10    13    16       0.650   0/1  -0.250 180/2   0.670   0/3
    26       14    10    13    16      -0.521   0/1  -2.018 180/2   1.996   0/3
    27       15    10    13    16      -0.521   0/1  -2.018 180/2   1.996   0/3
    28       10    13    16    17       0.650   0/1  -0.250 180/2   0.670   0/3
    29       10    13    16    18      -0.521   0/1  -2.018 180/2   1.996   0/3
    30       10    13    16    19      -0.521   0/1  -2.018 180/2   1.996   0/3
    31       13    16    17    20       0.468   0/3
    32       13    16    17    21       0.468   0/3
    33       13    16    17    22       0.468   0/3
    34       18    16    17    20       0.300   0/3
    35       18    16    17    21       0.300   0/3
    36       18    16    17    22       0.300   0/3
    37       19    16    17    20       0.300   0/3
    38       19    16    17    21       0.300   0/3
    39       19    16    17    22       0.300   0/3

Relvant lines from UNL_6B2B1D.itp (have added semicolons to denote the line I have mentioned above:

[ dihedrals ]
; PROPER DIHEDRAL ANGLES
;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
   10    9    6    2        3       1.715   2.845   1.046  -5.607  -0.000   0.000
   17   16   13   10        3       1.715   2.845   1.046  -5.607  -0.000   0.000
    9    6    2    1        3       1.715   2.845   1.046  -5.607  -0.000   0.000
   16   13   10    9        3       1.715   2.845   1.046  -5.607  -0.000   0.000
    9    6    2    8        3       1.590   4.770   0.000  -6.360  -0.000   0.000
   16   13   10   15        3       1.590   4.770   0.000  -6.360  -0.000   0.000
    9    6    2    7        3       1.590   4.770   0.000  -6.360  -0.000   0.000 ;;;;;
   16   13   10   14        3       1.590   4.770   0.000  -6.360  -0.000   0.000
    8    2    1    4        3       0.628   1.883   0.000  -2.510  -0.000   0.000
   15   10    9   12        3       0.628   1.883   0.000  -2.510  -0.000   0.000
    7    2    1    3        3       0.628   1.883   0.000  -2.510  -0.000   0.000
    7    2    1    4        3       0.628   1.883   0.000  -2.510  -0.000   0.000
   20   17   16   19        3       0.628   1.883   0.000  -2.510  -0.000   0.000
    7    2    1    5        3       0.628   1.883   0.000  -2.510  -0.000   0.000
   15   10    9   11        3       0.628   1.883   0.000  -2.510  -0.000   0.000
   14   10    9   12        3       0.628   1.883   0.000  -2.510  -0.000   0.000
    8    2    1    3        3       0.628   1.883   0.000  -2.510  -0.000   0.000
    8    2    1    5        3       0.628   1.883   0.000  -2.510  -0.000   0.000
   21   17   16   19        3       0.628   1.883   0.000  -2.510  -0.000   0.000
   22   17   16   18        3       0.628   1.883   0.000  -2.510  -0.000   0.000
   21   17   16   18        3       0.628   1.883   0.000  -2.510  -0.000   0.000
   14   10    9   11        3       0.628   1.883   0.000  -2.510  -0.000   0.000
   20   17   16   18        3       0.628   1.883   0.000  -2.510  -0.000   0.000
   22   17   16   19        3       0.628   1.883   0.000  -2.510  -0.000   0.000
   21   17   16   13        3       0.979   2.937   0.000  -3.916  -0.000   0.000
   15   10    9    6        3       0.979   2.937   0.000  -3.916  -0.000   0.000
   22   17   16   13        3       0.979   2.937   0.000  -3.916  -0.000   0.000
   20   17   16   13        3       0.979   2.937   0.000  -3.916  -0.000   0.000
   14   10    9    6        3       0.979   2.937   0.000  -3.916  -0.000   0.000
   18   16   13   10        3       1.590   4.770   0.000  -6.360  -0.000   0.000
   19   16   13   10        3       1.590   4.770   0.000  -6.360  -0.000   0.000
   12    9    6    2        3       1.590   4.770   0.000  -6.360  -0.000   0.000
   11    9    6    2        3       1.590   4.770   0.000  -6.360  -0.000   0.000
    6    2    1    5        3       0.979   2.937   0.000  -3.916  -0.000   0.000
   13   10    9   12        3       0.979   2.937   0.000  -3.916  -0.000   0.000
    6    2    1    4        3       0.979   2.937   0.000  -3.916  -0.000   0.000
    6    2    1    3        3       0.979   2.937   0.000  -3.916  -0.000   0.000
   13   10    9   11        3       0.979   2.937   0.000  -3.916  -0.000   0.000
   13   10    9    6        3      -1.151   1.151   0.000  -0.000  -0.000   0.000
```
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Depending on what force field you are planning to use, I would recommend trying to generate the topologies dihedrals listing with Topolbuild or BuildTop (http://www.gromacs.org/Downloads/User_contributions/Other_software). Let me know if I can be of any additional assistance.

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    $\begingroup$ Welcome to the site! Hopefully this will be useful to the OP, but it may help if you provide a little more information about either of these programs. $\endgroup$ – Tyberius May 6 at 18:18
  • $\begingroup$ -1 This does not answer the question. OP is asking about the conversion of dihedral parameters from tinker format to the gromacs. Topolbuild does not seem to do that. $\endgroup$ – Shoubhik R Maiti May 6 at 19:05
  • $\begingroup$ @ShoubhikRMaiti This user is brand new to Stack Exchange: What value do we get from downvoting them, that can't be obtained just by writing a comment? $\endgroup$ – Nike Dattani May 13 at 18:35
  • $\begingroup$ @NikeDattani It's just to offset the number of upvotes it has received. If bad answers receive upvotes here, that just sets a bad precedent. I understand that downvotes can scare off new users, but at the same time, poor/irrelevant answers cannot also be upvoted. If another person comes upon this page, and sees an upvoted answer, they will think it is right. Whereas writing a comment and downvoting would make them cautious before trusting the answer: this is my main motivation in doing so. $\endgroup$ – Shoubhik R Maiti May 13 at 18:38
  • 1
    $\begingroup$ @ShoubhikRMaiti This timeline: mattermodeling.stackexchange.com/posts/4944/… shows the "-1" comment came quite early. Perhaps we can give the user a chance to act on Tyberius's comment (which by the way was not associated with a downvote). $\endgroup$ – Nike Dattani May 13 at 18:42

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