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Input Files for Force Field X (FFX) Calculations

The FFX software package contains a very powerful and ever expanding library of functions to aid in a variety of computational chemistry endeavors. It is difficult to utilize FFX without properly formatted input files. The following is a brief and general guide on how to set up files for an FFX command.

Necessary Files

In general, FFX commands need coordinates to perform their function. The standard FFX coordinate file follows TINKER1 XYZ file format conventions (however most FFX commands also function with PDB files). The first line of an XYZ file contains the number of atoms within the structure followed by an identifier (this identifier is handled as a comment). Optionally, the next line can contain lattice parameters for a crystal that is produced with the provided coordinates (space group is specified within the properties file). Finally, the remaining lines consist of specific atoms. The atomic coordinate lines contain the following information from left to right: atom number, atomic label, x-coordinate, y-coordinate, z-coordinate, atom type, and bonded atoms. Contents of the file "CBZ.xyz" are provided below as an example: 


                    30 CBZ.xyz
                    10.32830623   10.95565862   17.24348658   90.00000000   86.28198726   90.00000000
                     1   O  3.80927596  1.34427638  0.60716888  415   14
                     2   N  2.81747690  1.03638807 -1.57326561  407    4    5   14
                     3   N  3.37765424 -0.75657908 -0.16702976  409   14   29   30
                     4   C  2.49090571  2.40659604 -1.86571082  402    2    6   10
                     5   C  2.03565503  0.12640028 -2.41840836  402    2    7   11
                     6   C  1.16225543  2.88826730 -1.49404155  406    4    8   12
                     7   C  0.60983897 -0.01518350 -2.33704738  406    5    9   13
                     8   C  0.21565062  2.02225648 -0.83539346  404    6    9   19
                     9   C -0.04625716  0.76418164 -1.25711359  404    7    8   20
                     10  C  3.39292036  3.28514942 -2.51085999  408    4   15   21
                     11  C  2.71013427 -0.70305940 -3.35553573  408    5   16   22
                     12  C  0.83676064  4.23291832 -1.76894534  403    6   17   23
                     13  C -0.06386162 -0.85693639 -3.23715672  403    7   18   24
                     14  C  3.36416024  0.61469239 -0.31033724  401    1    2    3
                     15  C  3.04253626  4.61212300 -2.74187904  405   10   17   25
                     16  C  2.02730138 -1.50085488 -4.23375119  405   11   18   26
                     17  C  1.79008186  5.10526234 -2.35301895  410   12   15   27
                     18  C  0.59592378 -1.57566716 -4.23801013  410   13   16   28
                     19  H -0.39097751  2.36441559 -0.00063083  414    8
                     20  H -0.88106295  0.23645393 -0.75844449  414    9
                     21  H  4.37373437  2.92419678 -2.72332680  412   10
                     22  H  3.74724689 -0.70451346 -3.34950963  412   11
                     23  H -0.18755136  4.59412309 -1.56957313  417   12
                     24  H -1.15698939 -0.82123003 -3.08699193  417   13
                     25  H  3.79716480  5.28962322 -3.13293051  416   15
                     26  H  2.53972796 -2.12433359 -4.91011776  416   16
                     27  H  1.47993023  6.10054327 -2.45187745  413   17
                     28  H  0.03252031 -2.28886293 -4.83185282  413   18
                     29  H  3.56217740 -1.12279241  0.76008088  411    3
                     30  H  3.35446649 -1.48152092 -0.86332390  411    3

In addition to a coordinate file, you will likely need a Properties file (analogous to a TINKER1 keyword file). Traditionally, these files have the same name as the coordinate file (e.g. CBZ.xyz would have either CBZ.properties or CBZ.key), however this file can also be specified from the commands line by adding "-Dkey=NAME.key" before your FFX command. Many specifications can be made within the Properties file (see here). One of the most important is either the "forcefield" or "parameters" variables as they control how to represent the supplied coordinates. The "forcefield" keyword specifies a given force field (e.g. "forcefield AMOEBA_BIO_2018", which is sufficient for most proteins). The "parameters" keyword references a stand-alone file containing force field parameters, scaling terms, and units. FFX can also augment a given force field with additional parameters using the "patch" variable. For example, atomic parameters for small molecules can be generated by auto-parameterization tools (e.g. PolType2 2,3 can be used to generate AMOEBA patch files). An example Properties file is below (CBZ.properties): 


                    forcefield AMOEBA_BIO_2018
                    patch /PATH/TO/CBZ.patch
                    spacegroup P1
                    a-axis 10.0
                    b-axis 10.0
                    c-axis 10.0
                    alpha 90.0
                    beta 90.0
                    gamma 90.0
                    vdw-cutoff 15.0

References:

1. J. A. Rackers, Z. Wang, C. Lu, M. L. Maury, L. Lagardère, M. J. Schnieders, J.-P. Piquemal, P. Ren, J. W. Ponder, (2018). Tinker 8: Software Tools for Molecular Design. J. Chem. Theory. Comput., 14 (10), 5273–5289 DOI: http://dx.doi.org/10.1021/acs.jctc.8b00529

2. Wu, J. C., Chattree, G., Ren, P. (2012). Automation of AMOEBA polarizable force field parameterization for small molecules. Theoretical chemistry accounts, 131(3), 1138. https://doi.org/10.1007/s00214-012-1138-6

3. Walker, B., Liu, C., Wait, E., Ren, P. (2022). Automation of AMOEBA polarizable force field parameterization for small molecules: Poltype 2. J. Comput. Chem. 2022, 43( 23), 1530. https://doi.org/10.1002/jcc.26954