The rrDNAv1 model is a reduced or simplified representation of DNA. The DNA is represented by a base unit consisting of three atoms per basepair (3DNA) or three atoms every four basepairs (3DNA4). The base unit is asymmetrical: 'Center' is located approximately at the midpoint of the line between the C1' atoms, 'Left' is 5Å from 'Center' towards one of the C1' atom and 'Front' is 2.5A from 'Center' towards the major groove and 90° from 'Left'. The ends of the chain may be joined to form a closed circle. The force field consists of four terms: Bonds, Angles, Impropers and SoftSphereX. The Bonds terms are partitioned into two lists, one to hold distance constraints, the other to hold the stretching terms along the length of the DNA. The Angles terms are also partitioned, one to hold the angle terms that mimic the roll and tilt rotations of the base plane and the other to hold constraints to keep the base plane rectangular and perpendicular to the bond that represents the longitudinal stretch. The Impropers term is used to represent the twisting of the baseplanes. The SoftSphereX term is used to prevent strand crossing; this makes it possible for a circular model to maintain a linking difference (even when only one DNA strand is represented). A chain may be homogeneous: every link in the chain is made up of the same kind of atom. Or, the chain may be heterogeneous: the atoms may be of different types. Modules are located within the Yup package at Yup/Models/rrDNAv1/. The FFA, Calculate and Analyzer modules are designed for public use while the other modules are not. Module Summary const Constants for the rrDNAv1 modules: constructor functions and labels for the force terms; the location of the parameter library and a table containing legal prefixes, atom inclusion types, atom exclusion types and atomic masses. params Structural parameters of the base unit for each of the four base type and for the undifferentiated base type. rr3dna Functions to add atoms and force field terms of the rrDNAv1 model tracechain A subclass of the TraceChain class; to generate starting structures: a straight line for open models, a closed circle for circular models and to follow the path of an existing structure. curves Prepare data for the Topology module; to calculate the Linking and Writhing numbers. internalC Link to the AutoGen module to generate internal coordinates. parmtop A subclass of the ParmTop class; used to generate a parmtop file out of a rrDNAv1 model. FFA Force Field Assembler Class and Function to create and manipulate rrDNAv1 models. Analyzer Functions to analyze rrDNAv1 models The const module defines the parameter library as Yup/Data/rrDNAv1/ (within the Yup package). However, the user can create and use a different library. In order to do this, first create a text file called source-of-constants in a previously empty directory. See FPF for the format of this document or copy it from the standard parameter library. Do not change the number of, or the names of, the inclusion and exclusion atom types. You can only modify existing interaction types (change the force field parameters), add new interaction types, or remove existing interaction types. (An interaction type is a combination of atom types, for example, a pair of atom types form a Bonds interaction type. It is necessary to define interaction types for all combinations that can occur in a model. At the same time, it is desirable to omit interaction types for illogical combinations, e.g., for two atom types that cannot form a bond.) When source-of-constants is ready, run the program Yup.fpf to convert it to a number of database files. Pass the path (to the enclosing directory) to the constructor function FFA(). The force field assembler is subclassed from the template Chains in Yup.Tools.Chains The force field assembler also make use of the functions in the LinSeq module which can also be found in Yup.Tools. Force Field Assembly Calculate Analysis Service Functions