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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: tutorial3.C,v 1.6.26.3 2007/05/25 09:36:29 oliver Exp $
//
#include <BALL/KERNEL/system.h>
#include <BALL/KERNEL/selector.h>
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/STRUCTURE/fragmentDB.h>
#include <BALL/STRUCTURE/residueChecker.h>
#include <BALL/MOLMEC/AMBER/amber.h>
#include <BALL/MOLMEC/MINIMIZATION/conjugateGradient.h>
#include <BALL/MOLMEC/MDSIMULATION/canonicalMD.h>
using namespace BALL;
int main()
{
// Read a structure from the PDB file
PDBFile infile("pdb4pti.ent");
System S;
infile >> S;
infile.close();
// Add the missing hydrogen atoms in a standard geometry,
// normalizee the names to be PDB compliant and construct
// missing bonds.
FragmentDB db("");
S.apply(db.normalize_names);
S.apply(db.add_hydrogens);
S.apply(db.build_bonds);
// Make sure we have a reasonable structure.
// The residue checker will print warnings for
// numerous common problems like missing atoms,
// overlaps, etc.
ResidueChecker rc(db);
S.apply(rc);
// Construct an AMBER force field object
// from our protein, select the added hydrogens
// only and optimize the hydrogen positions
// (heavy atoms will remain fixed (similar to
// a BELLY run in AMBER).
AmberFF amber(S);
Selector hydrogen_selector("element(H)");
S.apply(hydrogen_selector);
ConjugateGradientMinimizer cgm(amber);
cgm.setEnergyOutputFrequency(1);
cgm.setMaxGradient(1.0);
std::cout << "Minimizer options:" << std::endl ;
cgm.options.dump(std::cout);
cgm.minimize(300);
// Remove the selection again. We will now
// perform a full MD run in a water box.
S.deselect();
// We call the setup method of AmberFF again
// to add the missing water for the solvent box.
amber.options[PeriodicBoundary::Option::PERIODIC_BOX_ENABLED] = "true";
amber.options[PeriodicBoundary::Option::PERIODIC_BOX_ADD_SOLVENT] = "true";
amber.setup(S);
Log.info() << "Creating MDS..." << std::endl;
CanonicalMD md(amber);
md.setReferenceTemperature(300.0);
md.setBathRelaxationTime(0.0001);
md.setEnergyOutputFrequency(1);
md.simulateIterations(100);
std::cout << "Simulation settings:" << std::endl;
md.options.dump(std::cout);
// Store the final structure.
PDBFile final("final.pdb", File::MODE_OUT);
final << S;
final.close();
return 0;
}
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