Sequence file format


Card/Variable Format Description
I/1A1$ needed as search character
I/2A10Name of sequence
II/1I5Segment 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/2A10Segment name for 0 or positive segment number
II/3I5First link segment number
II/4I3First link segment link atom
II/5I5Second link segment number
II/6I3Second link segment link atom
II/7I5Third link segment number
II/8I3Third link segment link atom
II/9I5Fourth link segment number
II/10I3Fourth link segment link atom
II/11I5Fifth link segment number
II/12I3Fifth link segment link atom
II/13I5Sixth link segment number
II/14I3Sixth link segment link atom
II/15I5Seventh link segment number
II/16I3Seventh link segment link atom
II/17I5Eighth link segment number
II/18I3Eighth link segment link atom
II/19I5Ninth link segment number
II/20I3Ninth link segment link atom
II/21I5Tenth link segment number
II/22I3Tenth 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.