molecule m;
float x[990], fret;

m = getpdb( "FGrph-5hex_Reparam.pdb");
readparm( m, "FGrph-5hex_Reparam.prmtop" );
mm_options( "cut=999.0, ntpr=50" );

setxyz_from_mol(m, NULL, x);
mme_init( m, NULL, "::ZZZ", x, NULL);

//conjugate gradient minimization
conjgrad(x, 3*m.natoms, fret, mme, 0.001, 0.0001, 30000);

//Newton-Raphson minimization
mm_options( "ntpr=10" );
newton( x, 3*m.natoms, fret, mme, mme2, 0.00000001, 0.0, 500 );

//Output minimized structure
setmol_from_xyz( m, NULL, x);
putpdb( "FGrph-5hex_Reparam_min.pdb", m );

//get the normal modes:
nmode( x, 3*m.natoms, mme2, 990, 0, 0.0, 0.0, 0);


//
// nab nmode.nab 
// ./a.out > freq.txt
// eigenvectors are stored in vecs file and also reduced masses and information about frequencies and minimization is stored in freq.txt