Hi,
I am trying to write an itp file for the compound 1,2-diethoxyethance (CCOCCOCC) (attached pdb to this post).
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, F1 = -0.521, F2 = -2.018, F3 = 1.996, F4 = 0
I use the GROMACS formula:
c0 = (F2+(F1+F3)/2)*4.184 = -5.358
c1 = 0.5*(-F1+3F3)*4.184 = 13.617
c2 = (-F2 + 4*F4)*4.184 = 8.443
c3 = -2F3*4.184 = -16.7025
c4 = -4F4 = 0
c5 = 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
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.
Relevant part of f2.out:
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
Relevant part of UNL_6B2B1D.itp:
[ 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