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10
1 O 1.251722 -1.128767 0.434331 404 5 10
2 O 0.844886 1.092397 0.237216 406 5
3 N -1.815560 0.588102 -0.324599 403 4 8 9
4 C -0.849874 -0.492647 -0.449814 401 3 5 6 7
5 C 0.470594 -0.061298 0.132685 402 1 2 4
6 H -1.195550 -1.387129 0.076104 405 4
7 H -0.620445 -0.803981 -1.483080 405 4
8 H -2.537209 0.496409 -1.034572 407 3
9 H -1.333966 1.469038 -0.494689 407 3
10 H 2.154510 -0.772681 0.564391 408 1
Total atom number is on the first line.
The first column is the atom index.
The second column is the atomic symbol.
The 3 -5th columns are x,y,z coordinates in Angstrom.
The 6th is the “atom type” defined in the *.key file. This is the index tinker uses to assign parameters from the key/parameter file.
The 7th – last columns are lists of atom indices that are connected to the current atom index.
Final Key File
Atom Type Definitions Example
atom 404 404 O "glycine " 8 15.999 2
atom 406 406 O "glycine " 8 15.999 1
atom 403 403 N "glycine " 7 14.007 3
atom 401 401 C "glycine " 6 12.011 4
atom 402 402 C "glycine " 6 12.011 3
atom 405 405 H "glycine " 1 1.008 1
atom 407 407 H "glycine " 1 1.008 1
atom 408 408 H "glycine " 1 1.008 1
First number is the "type" number and the second number is the "class" number.
Multipole and Polarize parameters always use type numbers due to the highly specific electrostatic envioronment.
All other parameter types use "class" numbers and are less specific.
By default, poltype uses the same class numbers as type numbers.
Van der Waals Parameter Definitions Example
# matching SMARTS from molecule [['[#7](-[#6](-[#6])(-[#1])-[#1])(-[#1])-[#1]', [2]]] to SMARTS from parameter file [['[#7](-[#6](-[#6](-[H])(-[H])-[H])(-[H])-[H])(-[H])-[H]', [2]]] with tinker type descriptions [[('C', '"Ethyl Amine CH2"')]]
# [401] = [[4]]
vdw 401 3.8200 0.1010
All type lines have a line above indicating which indices it corresponds to ([401] = [[4]]), where type number 401 has indices of 4 that correspond to it.
This type of comment is a match to the amoeba09 database of parameters.
['#7(-[#1])-[#1]', [2]] the first item in this list is a SMARTS string matching to the input molecule, the second item in the list specifies which atom in order (start counting from 1 on the left) that the match for the vdW atom corresponds to.
[['#7(-[H])-[H]', [2]]] similarly, the first item in this list is a SMILES from a molecule in the amoeba09 database. The seocnd item in the list is the atom in the SMARTS that the match corresponds to.
[[('C', '"Ethyl Amine CH2"')]] this is a list of the atom class descriptions that are matched from the amoeba09 database
The first number in the vdW parameter line is radius and the second is the depth parameter
The first two class numbers are atoms in a trigonal center, the last two 0's are wild card atom classes for any other atom class in the trigonal center
The last number is the opbend force constant
Torsion Parameter Definitions Example
# matching SMARTS from molecule [['[*]~[*]~[*]~[*]', [1, 2, 3, 4]]] to SMARTS from parameter file [['[#6](-[H])(-[H])(-[H])-[#6](-[H])(-[H])(-[H])', [2, 1, 5, 6]]] with tinker type descriptions [[('H', '"Alkane H3C-"'), ('C', '"Alkane CH3-"'), ('C', '"Alkane CH3-"'), ('H', '"Alkane H3C-"')]]
# [403, 401, 402, 404] = [[3], [4], [5], [1]]
# Fitted from Fragment SMARTS [#6](-[#6](-[#8]-[H])=[#8])(-[#7](-[H])-[H])(-[H])-[H] torsion atom indexes = 7,1,2,3 with smarts torsion indices 5,2,3,4 from fragment 5_1_Index_0.mol
# torsion % [#6](-[#6](-[#8]-[H])=[#8])(-[#7](-[H])-[H])(-[H])-[H] % 5,2,3,4 % -3.883,-0.434,4.077
torsion 403 401 402 404 -3.883 0.0 1 -0.434 180.0 2 4.077 0.0 3
The line that starts with "Fitted from Fragment" , indicates which fragment the torsion parameters were derived from (from fragment 5_1_Index_0.mol) for debugging purposes
torsion atom indexes = 7,1,2,3, indicates the atom indices that the torsion belongs too in the fragment molecule
with smarts torsion indices 5,2,3,4 indicates the atom order in the SMARTS string corresponding to the torsion
The torsion parameter line reads as "F Angle Number", where F is the force constant for the cosine term, Angle is the phase angle for the cosine term and Number is the number corresponding to which cosine term (can be up to 6).
Example plot of energy (left axis) and WBO (right axis) vs dihedral angle (bottom axis) torsion RMSE(red,blue)=.85 kcal/mol, relative RMSE=.42 kcal/mol. Yellow curve represents WBO, the green curve is AMOEBA prefit total energy, the blue curve is QM total energy, the pink curve is the fitting numerical spline + AMOEBA prefit total energy and the red curve is AMOEBA postfit total energy with an additional minimization with new parameters before evaluating the final AMOEBA energies.
The post fit red curve should be similar to the blue QM curve if fitting was successful (evaulated by RMSE).
The pink curve and red curve should also be similar.
