This page describes the format of the Force Parameter file (FPF). Purpose The FPF contains definitions of Inclusion and Exclusion Atom Types and the force constants for terms in the potential energy that are indexed by Atom Types. The FPF is a formatted file, i.e., it contains readable text. This is not the form that is used by YUP. The FPF is converted (using Yup.fpf) into a number of unformatted files, one for the Atom Types and one for each term of the force field. (The Electrostatic terms do not make use of data from the FPF.) YUP expects to find the unformatted files in a directory whose path name is supplied by the user. A copy of the FPF source is usually kept in this directory to document the force field. Name While the FPF may be given any name, the program Yup.fpf expects the FPF to be named "source-of-constants". Header A FPF must have a proper header line. Header Annotations After the header line, the content of a FPF is treated mainly as text targeted to the human reader. An exception arises when the text is formatted in a specific way (next section). To avoid this circumstance, annotations are usually offset from the left side of each line. Data A line that starts with a colon ":" on column one signals the start of a section that contains data which will be processed. The colon is followed by a keyword which is an all-uppercase word. This signals a header line. The body of the data must follow immediately and in a strict format; the only variations allowed are white spaces (including blank lines). The section is complete when the terminal keyword ":END" is found. Data sections may appear in any order that make sense. A section that refers to a symbol defined in another section must follow the section that defines the symbol. The Exclusion Atom Type is used to index energy terms where all pair interactions are implied except those that appear in an Exclusion list. Atom Exclusion Types An Exclusion list force-field term such as the Exclusion list variant of the Soft Sphere Interaction term must be provided with data for all pairs of Atom Exclusion Types. Since an :A:B: pair is the same as a :B:A: pair only data from the upper half the interaction matrix is needed. Exclusion Soft Sphere Exclusion van der Waals Exclusion Swiss Cheese The Atom Inclusion Type is used to index energy terms that have no implied interactions; only those that are listed in an Inclusion list are calculated. Atom Inclusion Groups are sets of Atom Inclusion Types to collectively set parameter values. Atom Inclusion Types Atom Inclusion Groups A list of names (such as of a bonded atom pair) is written between colons and the names are separated by additional colons. For example, a trio of atom types is written like ":A:B:C:" and it describes an angle centered at an atom of type "B" flanked by atoms of types "A" and "C". Bonds Angles Torsions Improper Torsions Inclusion Soft Sphere Inclusion van der Waals Hand Hooke Distance NOE Each section may only appear once. More sections are on the way. Yup.fpf will produce a file for each force-field term, even for those terms that do not contain any data. If a model makes use of a force-field term, then the corresponding file must contain at least one set of constants. Atom Types The distinction between Inclusion and Exclusion Atom Types may be minimized by using the same set of names for both types and assigning the same type name to both the atomitype and atomxtype attributes of each atom. However, there is a strong incentive to keep the number of Exclusion types to a bare minimum, because of the requirement to provide data for all pairs of Exclusion Atom Types, The number of Atom (Exclusion or Inclusion) Types is limited to the largest unsigned integer that can fit in one quarter of the width of the word that is used to represent an unsigned long integer. Most machines today represent unsigned long integers in a 32-bit field; this limits the number of Atom Types to the largest unsigned integer that can be represented with 8 bits which is 28 or 256. One would expect that the limit on a 64-bit machine would be 216 or 65536 but this is almost never the case. Most 64-bit machines operate in a 32-bit compatible mode. Therefore, on nearly all machines there can only be 256 Atom Inclusion Types and 256 Atom Exclusion Types. Check The Yup.fpf program has a checking option. This generates output on the standard output (usually redirected to a file). Check Overview Exclusion Types Inclusion Types Exclusion Soft Spheres Exclusion van der Waals Bonds Angles Improper Torsions Distance NOE Torsion Power Series Exclusion Generalized LJ Header Check Inclusion Groups Inclusion Soft Spheres Inclusion van der Waals Hooke Hand Torsions Exclusion SwissCheese Angle NOE Inclusion Generalized LJ