void singlePoint()
{
double energy = amber.updateEnergy();
amber.updateForces();
Gradient grad;
grad.set(amber.getAtoms());
grad.normalize();
Log.info() << "single point energy: " << energy << " kJ/mol" << endl;
Log.info() << " - stretch :" << amber.getStretchEnergy() << " kJ/mol" << endl;
Log.info() << " - bend :" << amber.getBendEnergy() << " kJ/mol" << endl;
Log.info() << " - torsion :" << amber.getTorsionEnergy() << " kJ/mol" << endl;
Log.info() << " - VdW :" << amber.getVdWEnergy() << " kJ/mol" << endl;
Log.info() << " - electrostatic:" << amber.getESEnergy() << " kJ/mol" << endl;
Log.info() << "grad: " << grad.rms << endl;
}
int main(int argc, char** argv)
{
if (argc != 3)
{
Log.error() << argv[0] << " <pdb file A> <pdb file B>" << endl;
return 1;
}
// open the first PDB file
PDBFile pdb(argv[1]);
if (pdb.bad())
{
// if the file could not be opened, print error message and exit
Log.error() << "cannot open PBD file " << argv[1] << endl;
return 2;
}
// read the contents of the file A into a system
System A;
pdb >> A;
pdb.close();
// open the second PDB file
pdb.open(argv[2]);
if (pdb.bad())
{
// if the file could not be opened, print error message and exit
Log.error() << "cannot open PBD file " << argv[2] << endl;
return 2;
}
// read the contents of the file B into a system
System B;
pdb >> B;
pdb.close();
// normalize the names and build all bonds
Log.info() << "normalizing names and building bonds..." << endl;
FragmentDB db("");
A.apply(db.normalize_names);
A.apply(db.build_bonds);
B.apply(db.normalize_names);
B.apply(db.build_bonds);
// calculate the atomic contact energies of A and B
float ACE_A = calculateACE(A);
float ACE_B = calculateACE(B);
// calculate the electrostatic energies of A and B
AmberFF amber;
amber.options[AmberFF::Option::ASSIGN_CHARGES] = "true";
amber.options[AmberFF::Option::OVERWRITE_CHARGES] = "true";
amber.setup(A);
amber.updateEnergy();
float ES_A = amber.getESEnergy();
float C_A = calculateCoulomb(A);
amber.setup(B);
amber.updateEnergy();
float ES_B = amber.getESEnergy();
float C_B = calculateCoulomb(B);
// finally, join the to systems into a single system
cout << "atoms in A: " << A.countAtoms() << endl;
cout << "atoms in B: " << B.countAtoms() << endl;
A.splice(B);
cout << "final atoms: " << A.countAtoms() << endl;
float ACE_AB = calculateACE(A);
amber.setup(A);
amber.updateEnergy();
float ES_AB = amber.getESEnergy();
float C_AB = calculateCoulomb(A);
// print the resulting energies
cout << "ES energy of A: " << ES_A << endl;
cout << "ES energy of B: " << ES_B << endl;
cout << "ES energy of AB:" << ES_AB << endl;
cout << "C energy of A: " << C_A << endl;
cout << "C energy of B: " << C_B << endl;
cout << "C energy of AB:" << C_AB << endl;
cout << "change in atomic contact energy on binding: "
<< (ACE_AB - ACE_A - ACE_B) << " kJ/mol" << endl;
cout << "change in electrostatic energy on binding: "
<< (ES_AB - ES_A - ES_B) << " kJ/mol" << endl;
cout << "total binding free energy: "
<< (ACE_AB - ACE_A - ACE_B) + (ES_AB - ES_A - ES_B) << " kJ/mol" << endl;
// done
return 0;
}