Contents of fragment file

Given below is the contents of the fragment file for water. The first line is a comment line, the only important parameter is the NOCONNECT keyword, which indicates that the program should not try to make any connections to other residues/molecules. Then follow three lines, that define the orientation in space of the residue; they are not used for general fragments, but are relevant and important for amino acid residues and DNA nucleotides. Finally, for each atom in the molecule, there should be a line with its number in the fragment; its name to be used in PDB files; the AMBER forcefield atomtype; a dummy atomname; connections and coordinates (bond, angle, dihedral angle) to other atoms in the molecule that can be used to give the position of the atom if it is not present in the PDB file; the atomic charge; and after the exclamation mark (!) the connections to other atoms in this fragment, or other fragments in case of amino acid residues/DNA nucleotides. The current version does not use the latter connections yet, but the next version will probably use them.

HOH  Water molecule  NOCONNECT
   1   DUMM  DU    M      0   0   0       0.0000      0.0000      0.0000
   2   DUMM  DU    M      1   0   0       1.4490      0.0000      0.0000
   3   DUMM  DU    M      2   1   0       1.5220    111.1000      0.0000
   4   O     OW    O      0   0   0       0.0000      0.0000      0.0000  -0.8340  !  5  6
   5   H1    HW    H      4   0   0       0.9572      0.0000      0.0000   0.4170  !  4
   6   H2    HW    H      4   5   0       0.9572    104.5200      0.0000   0.4170  !  4