The energy of the soft sphere contact between atoms i and j, Ess-ij is: Ess-ij = Kss-ij[ dij - do-ij ]n, dij < do-ij and is zero for other distances. d is the distance between atoms i and j, Kss is the force constant and d0 is the contact distance. n is a variable power (should be even) that is specified during run time. This force term is available in two variants: Inclusion (described here) and Exclusion. The Soft Sphere Inclusion record must appear only after the Atom Inclusion Types have been defined. This record must also appear after the Atom Inclusion Group record if Groups are used in this record. The Soft Sphere Inclusion record has the following format: :SOFT-SPHERE-INCLUSION :Typei:Typei: Kss-ii d0-ii :Typei:Typej: Kss-ij d0-ij ... ... ... :END The opening and closing keywords, like all keywords, begin with a colon and start on column one of their respective lines. The body of the data section may contain any number of lines. A line may be empty or may contain a list of two Atom Inclusion Type or Group names followed by two numbers. The names are written amongst three colons; the colons are not part of the names. The first number is the force constant in units of kcal/mol/Ån. The second number is the contact distance in Å. Following the second number may be text to serve as comment. The comment must be separated, by white space, from the second number. A soft sphere type defined for Inclusion Atom Types :A:B: will serve equally well for a soft sphere interaction of Types :B:A:. Only the first instance of a definition of a soft sphere type will be saved. Subsequent definitions for the same soft sphere type will be silently ignored. Therefore, definitions using Groups should be placed at the end of the list so that the generic defintions do not override the specific definitions. The program Yup.fpf will expand Groups into their component Types, hash each pair of Types into a numerical code, and sort the codes. This forms the index table. The force constants are converted to internal units used by YUP and with the contact distances these numbers form the data table. The index and data tables are written to the unformatted file: "Soft Sphere Inclusion Constants". 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