molecule m; atom a; float m_xyz[2000]; float dgrad, fret; int ai, ier; m = getpdb_prm("gbrna.pdb", "oldff/leaprc.rna.ff94", "", 1); ai = 0; if(mytaskid==0) for( a in m ){ printf( "%5d %8.4f %8.4f\n", ai, a.charge, a.radius ); ai++; if( ai > 10 ) break; } // putpdb( "prmpqr", m, "-pqr" ); mm_options( "ntpr=1, gb=1, kappa=0.10395, rgbmax=99., cut=99.0, diel=C "); mme_init( m, NULL, "::Z", m_xyz, NULL); dgrad = 3*m.natoms*0.0001; setxyz_from_mol( m, NULL, m_xyz ); ier = conjgrad(m_xyz, 3*m.natoms, fret, mme, dgrad, 10.0, 1 );