# Sequence file format

Card/Variable | Format | Description
--- | --- | ---
I/1 | A1 | `$` needed as search character
I/2 | A10 | Name of sequence
II/1 | I5 | Segment number, or -1 to identify the end of a molecule, -2 to identify the end of the solute part of the system, -3 to identify the end of the sequence, or 0 to identify the solvent
II/2 | A10 | Segment name for 0 or positive segment number
II/3 | I5 | First link segment number
II/4 | I3 | First link segment link atom
II/5 | I5 | Second link segment number
II/6 | I3 | Second link segment link atom
II/7 | I5 | Third link segment number
II/8 | I3 | Third link segment link atom
II/9 | I5 | Fourth link segment number
II/10 | I3 | Fourth link segment link atom
II/11 | I5 | Fifth link segment number
II/12 | I3 | Fifth link segment link atom
II/13 | I5 | Sixth link segment number
II/14 | I3 | Sixth link segment link atom
II/15 | I5 | Seventh link segment number
II/16 | I3 | Seventh link segment link atom
II/17 | I5 | Eighth link segment number
II/18 | I3 | Eighth link segment link atom
II/19 | I5 | Ninth link segment number
II/20 | I3 | Ninth link segment link atom
II/21 | I5 | Tenth link segment number
II/22 | I3 | Tenth link segment link atom

Card I needs a $ as the first character, immediately followed by a 10 character identifying name for the system. These 11 characters are used as a search string by nwTOP. Any number of lines may preceed the first sequence card, for example to give a description of the sequence and its author.

Card II identifies an individual segment. Any number of Cards II can be specified. If solvent is specified it needs to be the last specified segment. If not given, first links are made automatically to the segment on the previous card, unless its segment number is negative. If not given, second links are made automatically to the segment on the next card, unless its segment number is negative.