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139 ■Control file（rigid.inp） EXE> INPUT TOPOLOGY= COORDINA= SETBOU= QUIT EXE> MD RIGIDM= NAMERM= INTEGR= LOOPLI= SETTIM= CPUTIM= UPDATE= TIMEST= OUTCOO= OUTTRJ= OUTLOG= LOGFOR= METHOD= SETTEM= INITIA= STARTT= RANDOM= CALCAP= RADCAP= FORCAP= FUNCAP= SETCEN= CUTMET= DIEFUN= CALV15= CALHYD= CALE5N= QUIT EXE> OUTPUT COORDINATE= QUIT EXE> END FORM PDB READ NAMETO= NAMECO= NAMEBO= YES indo_w4.rig VELO 10000 5000.0D0 3600000.0D0 20 2.0D0 1000 1000 1000 DETA CANONICAL 300.0D0 SET 300.0D0 654321 indo_w4.tpl indo_w4.pdb indo_w4.capbc ; Specify use of rigid body model ; Specify rigid body model file name ; Specify Velocity-Verlet method CALC 10.0 50.0 HARMonic YES RESA CONS CALC NOCALC NOCALC CUTLEN= DIEVAL= CALE15= CALV5N= CALH5N= 12.0D0 1.0D0 CALC NOCALC NOCALC PDB NAMECO= indo_w4md.pdb myPresto 4.2
