nwTOP

# Topology generator nwTOP

The topology describes all static information that describes a molecular system. This includes the connectivity, such as bond-stretching, angle-bending and torsional interactions, as well as non-bonded interactions, such as van der Waals and Coulombic interactions.

The topology of a molecular system is generated by the topology generator nwTOP. The molecular system is described in terms of segments taken out of a database of predefined segments. Segments that are not available in one of the database files can be generated bye a utility program nwSGM.

The command line to run nwTOP is

`nwtop project forcefield`

where project is the name of a sequence on one of the sequence databases or a local file project.seq, and forcefield is the name of one of the available force fields. Force field parameters are taken from the parameter databases, or from a local file project.par is present. The format of the parameter file is identical to the ARGOS parameter file format. The resulting topology file is project.top

The input for nwTOP is taken from a sequence database, or given in a formatted sequence file project.seq. A sequence file may be appended to a sequence database. The format of a sequence file is slightly different from the ARGOS sequence file format.