private void loadBondedParams() {
String fileName = "res/amber03/ffbonded.itp";
List<String> fileAsList = FileReader.readFile(fileName);
int bondtypes = fileAsList.indexOf("[ bondtypes ]");
int constrainttypes = fileAsList.indexOf("[ constrainttypes ]");
int angletypes = fileAsList.indexOf("[ angletypes ]");
int improperDihedral = fileAsList.indexOf("[ dihedraltypes ]");
int properDihedral = fileAsList.lastIndexOf("[ dihedraltypes ]");
// System.out.println(bondtypes);
// System.out.println(constrainttypes);
// System.out.println(angletypes);
// System.out.println(improperDihedral);
// System.out.println(properDihedral);
loadBondParams(fileAsList.subList(bondtypes + 1, constrainttypes));
loadAngleParams(fileAsList.subList(angletypes + 1, improperDihedral));
loadImproperDihedralParams(fileAsList.subList(improperDihedral + 1, properDihedral));
loadProperDihedralParams(fileAsList.subList(properDihedral + 1, fileAsList.size()));
}
private void loadNonBondedParams() {
String fileName = "res/amber03/ffnonbonded.itp";
List<String> fileAsList = FileReader.readFile(fileName);
int atomtypes = fileAsList.indexOf("[ atomtypes ]");
loadVdParams(fileAsList.subList(atomtypes + 1, fileAsList.size()));
}