molecule m; float x[17247], fret, ier; m = getpdb_prm( "snap1.pdb","leaprc.ff99", "", 0 ); mm_options( "cut=999.0, ntpr=1, gb=1, gbsa=0" ); 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, 10000); printf("congrad returns %d\n",ier); //Newton-Raphson minimization mm_options( "ntpr=1" ); newton( x, 3*m.natoms, fret, mme, mme2, 0.00000001, 0.0, 10 ); //get the normal modes: nmode( x, 3*m.natoms, mme2, 0);