42 if (!top->isRigid()) {
43 bool isRigid = top->Rigidify();
48 std::cout << std::endl <<
"... ... System is already rigidified.";
50 std::cout << std::endl;
55 for (pit = nblist.
begin(); pit != nblist.
end(); pit++) {
59 if ((*pit)->getId() == -1) {
61 std::string pairId = boost::lexical_cast<std::string>((*pit)->getId());
62 std::string pdbname =
"Pair" + pairId +
".pdb";