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#include "Molmodel.h"
#include <iostream>
#include <exception>
#include <fstream>
using namespace SimTK;
int main() {
try {
// Load the PDB file and construct the system.
CompoundSystem system;
SimbodyMatterSubsystem matter(system);
DecorationSubsystem decorations(system);
DuMMForceFieldSubsystem forceField(system);
forceField.loadAmber99Parameters();
std::string pdb;
std::ifstream pdbFile("1AKGtrim.pdb");
pdbFile >> pdb;
Protein protein(pdb);
protein.assignBiotypes();
system.adoptCompound(protein);
system.modelCompounds();
system.addEventHandler(new VelocityRescalingThermostat(
system, 293.15, 0.1));
// Show me a movie
Visualizer viz(system);
system.addEventReporter( new Visualizer::Reporter(viz, 0.025) );
system.realizeTopology();
// Create an initial state for the simulation.
State state = system.getDefaultState();
LocalEnergyMinimizer::minimizeEnergy(system, state, 15.0);
// Simulate it.
VerletIntegrator integ(system);
integ.setAccuracy(1e-2);
TimeStepper ts(system, integ);
ts.initialize(state);
ts.stepTo(10.0);
return 0;
}
catch(const std::exception& e) {
std::cerr << "ERROR: " << e.what() << std::endl;
return 1;
}
catch(...) {
std::cerr << "ERROR: An unknown exception was raised" << std::endl;
return 1;
}
}
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