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);