3.1.5.19 RTF Generate Command

Syntax

                      { ANGLES               }
                      { THETAS               }
                      { { TORSIONS } [ ALL ] }
     GENERATE repeat( { { PHIS     } [ ONE ] }
                      { DONORS               }
                      { ACCEPTORS            }
                      { BILDS                }
                      { BUILDS               }
                      { ALL                  }

Function

The GENERATE command may be used to automatically generate parts of the topology file. Angles, torsions, donors, acceptors, and IC constructors may be generated either singly or in any combination. ALL specifies that all of these entities be constructed. Automatic generation is only performed with the atoms defined within a residue. Atoms involved with linkages to other atoms are not used in the automatic generation process, and must be generated “by hand”.

The bond angle construction works by examining the current list of bonds for the current residue, and generating angles for all pairs of bonds. The torsion angle construction can work in either of two ways. If the ALL suboption is specified, then for each bond, a torsion angle is constructed for all combinations of atoms attached to this torsion. If the ONE suboption is specified, the program will first look for a pair of heavy atoms attached to the central bond, and failing that, it will repeat the search looking at all atoms including hydrogens. The donors and acceptors generation depend on the use specifying which atom types are donors or acceptors in the MASS command above.

The generation of IC constructors is the most difficult generation task, and it is done primarily to provide a set of constructors which can be edited for better results. The program will first find three atoms connected together. Next, it will look at the central atom and see if an adjacent atom needs to be constructed. If so, it will generate a improper torsion constructor. It will then recursively try the new atom in conjunction with the previous two. Once these constructions complete, the program will attempt to add atoms on each end of the original three atoms, and will recurse on any successful constructions.

Because not all of these automatic generation commands work perfectly, there exists two mechanisms to edit the results. First, the RTF may be written out in free field format using a WRITE RTF CARD command and the result can be edited. Second, the DELETE options in other commands may be used to delete particular entries after they are generated. Also, additional entries for a residue may be made after the GENERATE command is given.

Note that non-bonded exclusions are generated automatically by default. See Nbxmod, for more information.