molecule m;
float xyz[4000], fret;
file file1;
file1=fopen("out.traj","w");

m = getpdb ("3jvs_wat_box.pdb");
readparm(m,"3jvs_wat_box.prmtop");
mm_options( "cut=999., ntpr=50, ntwx=1, nsnb=99999, diel=C, gb=1, dielc=1.0 , wcons=10000" );
setxyz_from_mol( m,NULL, xyz );
mme_init( m,"::H*" , "::!@H=", xyz, file1 );

// conjugate gradient minimization
conjgrad(xyz, 3*m.natoms, fret, mme, 0.1, 0.001, 200 );

// Newton-Raphson minimization\fP
mm_options( "ntpr=1" );
newton( xyz, 3*m.natoms, fret, mme, mme2, 0.00000001, 0.0, 50 );

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

fclose(file1);