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#include "SimTKmolmodel.h"
#include "SimTKsimbody_aux.h" // for vtk visualization
#include <iostream>
#include <fstream>
#include <exception>
using namespace SimTK;
using namespace std;
int main() { try
{
CompoundSystem system; // molecule-specialized simbody System
SimbodyMatterSubsystem matter(system);
DecorationSubsystem decorations(system);
TinkerDuMMForceFieldSubsystem dumm(system); // molecular force field
dumm.loadAmber99Parameters();
ifstream rnaFile("1L2X.pdb");
PdbStructure rnaStructure(rnaFile);
RNA rna( rnaStructure );
rna.assignBiotypes();
system.adoptCompound(rna);
system.updDefaultSubsystem().addEventReporter(
new VTKEventReporter(system, 0.020));
system.modelCompounds(); // finalize multibody system
State state = system.realizeTopology();
// Simulate it.
VerletIntegrator integ(system);
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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