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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: amberEnergy.C,v 1.9.28.1 2007/08/06 16:22:06 oliver Exp $
//
#include <BALL/MOLMEC/AMBER/amber.h>
#include <BALL/STRUCTURE/fragmentDB.h>
#include <BALL/STRUCTURE/residueChecker.h>
#include <BALL/FORMAT/PDBFile.h>
using namespace BALL;
using namespace std;
int main(int argc, char** argv)
{
Log.setPrefix(cout, "[%T]: ");
Log.setPrefix(cerr, "[%T]: ERROR: ");
// issue a usage hint if called without parameters
if ((argc < 2) || (argc > 4))
{
Log.error() << argv[0] << " <pdb file> [<option file>]" << endl;
return 1;
}
// open the PDB file
PDBFile pdb(argv[1]);
if (!pdb)
{
// 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 into a system
System S;
pdb >> S;
pdb.close();
// normalize the names and build all bonds
Log.info() << "normalizing names..." << endl;
FragmentDB db("");
S.apply(db.normalize_names);
Log.info() << "building bonds..." << endl;
S.apply(db.build_bonds);
Log.info() << "adding H..." << endl;
S.apply(db.add_hydrogens);
Log.info() << "checking residues..." << endl;
ResidueChecker rc(db);
S.apply(rc);
// create an AMBER force field and set its options from a file
AmberFF amber;
if (argc > 2)
{
amber.options.readOptionFile(argv[2]);
}
// setup the force field
Log.info() << "setting up force field..." << endl;
amber.setup(S);
// calculate the total energy and print it
Log.info() << "total energy: " << amber.updateEnergy() << " kJ/mol ";
Log.info() << "stretch: " << amber.getStretchEnergy() << " kJ/mol "
<< "bend: " << amber.getBendEnergy() << " kJ/mol "
<< "torsion: " << amber.getTorsionEnergy() << " kJ/mol "
<< "ES: " << amber.getESEnergy() << " kJ/mol "
<< "vdW: " << amber.getVdWEnergy() << " kJ/mol"
<< endl;
// alternatively
Log.info() << amber.getResults() << endl;
// done
return 0;
}
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