molecule m;
float x[573], fret, ier;

m = getpdb_prm( "snapshot_lig.pdb.3", "leaprc", "", 0 );
//readparm(m, "6ssDNA.top");
mm_options("rgbmax=100., cut=100.0, ntpr=50, nsnb=999, gb=0, diel=C");
mme_init( m, NULL, "::z", x, NULL);
setxyz_from_mol(m, NULL, x);

//conjugate gradient minimization
ier = conjgrad(x, 3*m.natoms, fret, mme, 0.1, 0.001, 4000);
printf( "conjgrad returns %d\n", ier );

//Newton-Raphson minimization
mm_options( "ntpr=1" );
ier = newton( x, 3*m.natoms, fret, mme, mme2, 0.0000001, 0.0, 0 );
printf( "newton returns %d\n", ier );

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