7
$\begingroup$

I have been playing with a polymer called glyme, and I have run Tinker analyze on it to get OPLS-AA parameters for it. I have attached the output parameter file to this post.

My question is, how do I go from the parameters given in the Tinker parameter file (ff.out) under "Improper Torsion Parameters" and "Torsional Angle Parameters" and translate those into a GROMACS topology file (UNL_4E9C7F.itp)? Both of these files are for benzene. Getting the bond and angle constants was a simple unit change but how does it work for the IMPROPER DIHEDRAL ANGLES?

The Improper Torsion Parameters according to the Tinker file are:

Amplitude = 1.667, Phase = 180.0, Periodicity = 2

Under IMPROPER DIHEDRAL ANGLES, I see that:

Phase = 180.0, Phase = 180.0, Periodicity = 2

However, how do I make the change? Similarly, for IMPROPER DIHEDRAL ANGLES, is there a way to convert the Torsional Angle Parameters? I would appreciate any advice you have for me!

this is the tinker file:


     ######################################################################
   ##########################################################################
  ###                                                                      ###
 ###            Tinker  ---  Software Tools for Molecular Design            ###
 ##                                                                          ##
 ##                       Version 8.8.3  November 2020                       ##
 ##                                                                          ##
 ##               Copyright (c)  Jay William Ponder  1990-2020               ##
 ###                           All Rights Reserved                          ###
  ###                                                                      ###
   ##########################################################################
     ######################################################################


 Interactions and Sites :

 Atomic Sites                                  12
 Bond Stretches                                12
 Angle Bends                                   18
 Improper Torsions                             18
 Torsional Angles                              24
 Van der Waals Sites                           12
 Atomic Partial Charges                        12

 Atom Definition Parameters :

   Atom  Symbol  Type  Class  Atomic   Mass  Valence  Description

     1     C       90     48     6    12.011    3     Aromatic C              
     2     C       90     48     6    12.011    3     Aromatic C              
     3     C       90     48     6    12.011    3     Aromatic C              
     4     C       90     48     6    12.011    3     Aromatic C              
     5     C       90     48     6    12.011    3     Aromatic C              
     6     C       90     48     6    12.011    3     Aromatic C              
     7     H       91     49     1     1.008    1     Aromatic H-C            
     8     H       91     49     1     1.008    1     Aromatic H-C            
     9     H       91     49     1     1.008    1     Aromatic H-C            
    10     H       91     49     1     1.008    1     Aromatic H-C            
    11     H       91     49     1     1.008    1     Aromatic H-C            
    12     H       91     49     1     1.008    1     Aromatic H-C            

 Bond Stretching Parameters :

          Atom Numbers                         KS       Bond

     1        1     2                      469.000    1.4000
     2        1     6                      469.000    1.4000
     3        1     7                      367.000    1.0800
     4        2     3                      469.000    1.4000
     5        2     8                      367.000    1.0800
     6        3     4                      469.000    1.4000
     7        3     9                      367.000    1.0800
     8        4     5                      469.000    1.4000
     9        4    10                      367.000    1.0800
    10        5     6                      469.000    1.4000
    11        5    11                      367.000    1.0800
    12        6    12                      367.000    1.0800

 Angle Bending Parameters :

             Atom Numbers                      KB      Angle   Fold    Type

     1        2     1     6                 63.000   120.000
     2        2     1     7                 35.000   120.000
     3        6     1     7                 35.000   120.000
     4        1     2     3                 63.000   120.000
     5        1     2     8                 35.000   120.000
     6        3     2     8                 35.000   120.000
     7        2     3     4                 63.000   120.000
     8        2     3     9                 35.000   120.000
     9        4     3     9                 35.000   120.000
    10        3     4     5                 63.000   120.000
    11        3     4    10                 35.000   120.000
    12        5     4    10                 35.000   120.000
    13        4     5     6                 63.000   120.000
    14        4     5    11                 35.000   120.000
    15        6     5    11                 35.000   120.000
    16        1     6     5                 63.000   120.000
    17        1     6    12                 35.000   120.000
    18        5     6    12                 35.000   120.000

 Improper Torsion Parameters :

                 Atom Numbers           Amplitude, Phase and Periodicity

     1        2     6     1     7               1.667   180.0   2
     2        6     7     1     2               1.667   180.0   2
     3        7     2     1     6               1.667   180.0   2
     4        1     3     2     8               1.667   180.0   2
     5        3     8     2     1               1.667   180.0   2
     6        8     1     2     3               1.667   180.0   2
     7        2     4     3     9               1.667   180.0   2
     8        4     9     3     2               1.667   180.0   2
     9        9     2     3     4               1.667   180.0   2
    10        3     5     4    10               1.667   180.0   2
    11        5    10     4     3               1.667   180.0   2
    12       10     3     4     5               1.667   180.0   2
    13        4     6     5    11               1.667   180.0   2
    14        6    11     5     4               1.667   180.0   2
    15       11     4     5     6               1.667   180.0   2
    16        1     5     6    12               1.667   180.0   2
    17        5    12     6     1               1.667   180.0   2
    18       12     1     6     5               1.667   180.0   2

 Torsional Angle Parameters :

                 Atom Numbers           Amplitude, Phase and Periodicity

     1        6     1     2     3       7.250 180/2
     2        6     1     2     8       7.250 180/2
     3        7     1     2     3       7.250 180/2
     4        7     1     2     8       7.250 180/2
     5        2     1     6     5       7.250 180/2
     6        2     1     6    12       7.250 180/2
     7        7     1     6     5       7.250 180/2
     8        7     1     6    12       7.250 180/2
     9        1     2     3     4       7.250 180/2
    10        1     2     3     9       7.250 180/2
    11        8     2     3     4       7.250 180/2
    12        8     2     3     9       7.250 180/2
    13        2     3     4     5       7.250 180/2
    14        2     3     4    10       7.250 180/2
    15        9     3     4     5       7.250 180/2
    16        9     3     4    10       7.250 180/2
    17        3     4     5     6       7.250 180/2
    18        3     4     5    11       7.250 180/2
    19       10     4     5     6       7.250 180/2
    20       10     4     5    11       7.250 180/2
    21        4     5     6     1       7.250 180/2
    22        4     5     6    12       7.250 180/2
    23       11     5     6     1       7.250 180/2
    24       11     5     6    12       7.250 180/2

 Van der Waals Parameters :

          Atom Number       Size   Epsilon   Size 1-4   Eps 1-4   Reduction

     1        1           3.5500    0.0700
     2        2           3.5500    0.0700
     3        3           3.5500    0.0700
     4        4           3.5500    0.0700
     5        5           3.5500    0.0700
     6        6           3.5500    0.0700
     7        7           2.4200    0.0300
     8        8           2.4200    0.0300
     9        9           2.4200    0.0300
    10       10           2.4200    0.0300
    11       11           2.4200    0.0300
    12       12           2.4200    0.0300

 Atomic Partial Charge Parameters :
                                             Neighbor   Cutoff
          Atom Number             Charge       Site      Site

     1        1                  -0.1150
     2        2                  -0.1150
     3        3                  -0.1150
     4        4                  -0.1150
     5        5                  -0.1150
     6        6                  -0.1150
     7        7                   0.1150
     8        8                   0.1150
     9        9                   0.1150
    10       10                   0.1150
    11       11                   0.1150
    12       12                   0.1150

This is itp file I obtained from LigParGen:


;
; GENERATED BY LigParGen Server
; Jorgensen Lab @ Yale University 
;
[ atomtypes ]
  opls_804  C804    12.0110     0.000    A    3.55000E-01   2.92880E-01
  opls_803  C803    12.0110     0.000    A    3.55000E-01   2.92880E-01
  opls_811  H811     1.0080     0.000    A    2.42000E-01   1.25520E-01
  opls_809  H809     1.0080     0.000    A    2.42000E-01   1.25520E-01
  opls_810  H810     1.0080     0.000    A    2.42000E-01   1.25520E-01
  opls_805  C805    12.0110     0.000    A    3.55000E-01   2.92880E-01
  opls_802  C802    12.0110     0.000    A    3.55000E-01   2.92880E-01
  opls_806  H806     1.0080     0.000    A    2.42000E-01   1.25520E-01
  opls_808  H808     1.0080     0.000    A    2.42000E-01   1.25520E-01
  opls_800  C800    12.0110     0.000    A    3.55000E-01   2.92880E-01
  opls_807  H807     1.0080     0.000    A    2.42000E-01   1.25520E-01
  opls_801  C801    12.0110     0.000    A    3.55000E-01   2.92880E-01
[ moleculetype ]
; Name               nrexcl
UNL                   3
[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  
     1   opls_800      1    UNL   C00      1    -0.1374    12.0110 
     2   opls_801      1    UNL   C01      1    -0.1375    12.0110 
     3   opls_802      1    UNL   C02      1    -0.1374    12.0110 
     4   opls_803      1    UNL   C03      1    -0.1372    12.0110 
     5   opls_804      1    UNL   C04      1     -0.137    12.0110 
     6   opls_805      1    UNL   C05      1    -0.1371    12.0110 
     7   opls_806      1    UNL   H06      1     0.1374     1.0080 
     8   opls_807      1    UNL   H07      1     0.1374     1.0080 
     9   opls_808      1    UNL   H08      1     0.1374     1.0080 
    10   opls_809      1    UNL   H09      1     0.1374     1.0080 
    11   opls_810      1    UNL   H0A      1      0.137     1.0080 
    12   opls_811      1    UNL   H0B      1      0.137     1.0080 
[ bonds ]
    2     1     1      0.1400 392459.200
    3     2     1      0.1400 392459.200
    4     3     1      0.1400 392459.200
    5     4     1      0.1400 392459.200
    6     1     1      0.1400 392459.200
    7     1     1      0.1080 307105.600
    8     2     1      0.1080 307105.600
    9     3     1      0.1080 307105.600
   10     4     1      0.1080 307105.600
   11     5     1      0.1080 307105.600
   12     6     1      0.1080 307105.600
    6     5     1      0.1400 392459.200

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3 
    1     2     3     1    120.000    527.184
    2     3     4     1    120.000    527.184
    3     4     5     1    120.000    527.184
    2     1     6     1    120.000    527.184
    2     1     7     1    120.000    292.880
    1     2     8     1    120.000    292.880
    2     3     9     1    120.000    292.880
    3     4    10     1    120.000    292.880
    4     5    11     1    120.000    292.880
    1     6    12     1    120.000    292.880
    6     5    11     1    120.000    292.880
    6     1     7     1    120.000    292.880
    5     6    12     1    120.000    292.880
    5     4    10     1    120.000    292.880
    1     6     5     1    120.000    527.184
    4     3     9     1    120.000    292.880
    4     5     6     1    120.000    527.184
    3     2     8     1    120.000    292.880

[ dihedrals ]
; IMPROPER DIHEDRAL ANGLES 
;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
    12     6     1     5    4        180.000     10.460     2  
    11     5     4     6    4        180.000     10.460     2  
    10     4     3     5    4        180.000     10.460     2  
     9     3     2     4    4        180.000     10.460     2  
     8     2     1     3    4        180.000     10.460     2  
     7     1     2     6    4        180.000     10.460     2  

[ dihedrals ]
; PROPER DIHEDRAL ANGLES
;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
    4    3    2    1        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
    5    4    3    2        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
    6    1    2    3        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
    4    5    6    1        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
    6    5    4    3        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
    5    6    1    2        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   12    6    1    2        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
    7    1    6    5        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   11    5    6    1        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   10    4    5    6        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   11    5    4    3        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   12    6    5    4        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
    9    3    2    1        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
    7    1    2    3        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
    8    2    1    6        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   10    4    3    2        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
    8    2    3    4        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
    9    3    4    5        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   10    4    3    9        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   12    6    1    7        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   12    6    5   11        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
    9    3    2    8        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
    8    2    1    7        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   11    5    4   10        3      30.334   0.000  -30.334  -0.000  -0.000   0.000

[ pairs ]
     1     4    1
     2     5    1
     3     6    1
     3     7    1
     1     9    1
     5     7    1
     4     8    1
     2    10    1
     1    11    1
     6     8    1
     5     9    1
     3    11    1
     2    12    1
     7     8    1
     6    10    1
     4    12    1
     8     9    1
     9    10    1
     7    12    1
    10    11    1
    11    12    1
```
$\endgroup$
7
  • $\begingroup$ just a wild guess, but have you looked at the parmed package? $\endgroup$
    – Cody Aldaz
    Apr 22 at 4:45
  • $\begingroup$ Thank you for your response, but I have not @CodyAldaz. I don't seem to find a way to make the conversion using parmed either. $\endgroup$
    – megamence
    Apr 22 at 13:05
  • $\begingroup$ Do you need to convert between the two or are you just trying to check how the parameters are used for each software? $\endgroup$
    – S R Maiti
    Apr 22 at 14:17
  • $\begingroup$ I am trying to convert between the two @ShoubhikRMaiti $\endgroup$
    – megamence
    Apr 22 at 14:20
  • 1
    $\begingroup$ @ShoubhikRMaiti manual.gromacs.org/current/reference-manual/functions/…, in this page, they also try to show how to go from OPLS parameters to GMX parameters for Proper Dihedrals. My question is, how does phase and amplitude come in to these formulae? $\phi$ is the actual dihedral angle, not the phase... $\endgroup$
    – megamence
    Apr 22 at 17:23
5
$\begingroup$

This is actually a straightforward problem about unit conversions and careful manipulation based on the functional forms of the potential we want.

To go from the Improper Torsion Parameters to the Improper Dihedral in GROMACS, simply do the following transformation on the amplitude: $\textrm{ampl}\times 4.184\times n/2~$ where 4.184 is the unit conversion factor from kcal to kJ, and $n$ is the number of times that torsion is repeated in the table.

To go from the Torsional Angle Parameters to the GROMACS itp file, make the changes as per the ones given in the GROMACS page, equations 33:

\begin{split}\displaystyle \begin{eqnarray} \displaystyle C_0&=&F_2 + \frac{1}{2} (F_1 + F_3)\tag{1}\\ \displaystyle C_1&=&\frac{1}{2} (- F_1 + 3 \, F_3)\tag{2}\\ \displaystyle C_2&=& -F_2 + 4 \, F_4\tag{3}\\ \displaystyle C_3&=&-2 \, F_3\tag{4}\\ \displaystyle C_4&=&-4 \, F_4\tag{5}\\ \displaystyle C_5&=&0\tag{6}. \end{eqnarray}\end{split}

$\endgroup$
1
  • 2
    $\begingroup$ +1 and thank you so much for coming back and sharing the answer here so that others may benefit from it in the future! I've just made some small edits to keep this answer within the format consistent with the rest of the site. Also, the green checkmark for "accepting" an answer doesn't do much help on self-answers: it does not give you the +2 points and does not put the answer to the top of the list of answers, all it does it show the green checkmark and discourage others from giving alternative answers which might even be more insightful, so I don't usually recommend accepting self-answers. $\endgroup$ Apr 26 at 18:16

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