molecule m;
float x[1080], fret;

m = getpdb("G17-vac-min.pdb"); 
readparm("m,"G17-vac.top");
getxyz("G17-vac-min.rst",360,x);

mm_options("cut=12, ntpr=1, nsnb=99999, diel=C, gb=0, dielc=1.0");
mme_init(m, NULL, "::Z", x, NULL);
setxyz_from_mol(m, NULL, x);

//conjugate gradient minimization
conjgrad(x,3*m.natoms,fret,mme,0.001,0.001,20000);

//newton-raphson minimization
newton(x,3*m.natoms,fret,mme,mme2,0.0000001,0.0,1000);

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