chemistry@chemistry-desktop:~/Desktop$ tleap -I: Adding /home/chemistry/amber12/dat/leap/prep to search path. -I: Adding /home/chemistry/amber12/dat/leap/lib to search path. -I: Adding /home/chemistry/amber12/dat/leap/parm to search path. -I: Adding /home/chemistry/amber12/dat/leap/cmd to search path. Welcome to LEaP! (no leaprc in search path) > source /home/chemistry/amber12/dat/leap/cmd/leaprc.ff99SB ----- Source: /home/chemistry/amber12/dat/leap/cmd/leaprc.ff99SB ----- Source of /home/chemistry/amber12/dat/leap/cmd/leaprc.ff99SB done Log file: ./leap.log Loading parameters: /home/chemistry/amber12/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 Loading parameters: /home/chemistry/amber12/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) Loading library: /home/chemistry/amber12/dat/leap/lib/all_nucleic94.lib Loading library: /home/chemistry/amber12/dat/leap/lib/all_amino94.lib Loading library: /home/chemistry/amber12/dat/leap/lib/all_aminoct94.lib Loading library: /home/chemistry/amber12/dat/leap/lib/all_aminont94.lib Loading library: /home/chemistry/amber12/dat/leap/lib/ions94.lib Loading library: /home/chemistry/amber12/dat/leap/lib/solvents.lib > loadamberparams /home/chemistry/amber12/dat/leap/parm/parm99_mod.dat Loading parameters: /home/chemistry/amber12/dat/leap/parm/parm99_mod.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 > loadamberparamsheme.frcmod ERROR: syntax error > loadamberparams heme.frcmod Loading parameters: ./heme.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here Unknown keyword: in parameter file. Perhaps a format error? Unknown keyword: in parameter file. Perhaps a format error? Unknown keyword: in parameter file. Perhaps a format error? > loadamberparams hemeall.in Loading parameters: ./hemeall.in Reading force field modification type file (frcmod) Reading title: 0 0 2 Unknown keyword: in parameter file. Perhaps a format error? Unknown keyword: Heme r in parameter file. Perhaps a format error? Unknown keyword: heme_all.d in parameter file. Perhaps a format error? Unknown keyword: HEM INT in parameter file. Perhaps a format error? Unknown keyword: CORRECT O in parameter file. Perhaps a format error? Unknown keyword: 0.50000 in parameter file. Perhaps a format error? Unknown keyword: 1 DUM in parameter file. Perhaps a format error? Unknown keyword: 2 DUM in parameter file. Perhaps a format error? Unknown keyword: 3 DUM in parameter file. Perhaps a format error? Unknown keyword: 19 FE in parameter file. Perhaps a format error? Unknown keyword: 20 NA in parameter file. Perhaps a format error? Unknown keyword: 21 C1A in parameter file. Perhaps a format error? Unknown keyword: 22 C2A in parameter file. Perhaps a format error? Unknown keyword: 23 CAA in parameter file. Perhaps a format error? Unknown keyword: 24 HP7 in parameter file. Perhaps a format error? Unknown keyword: 25 HP7 in parameter file. Perhaps a format error? Unknown keyword: 26 CBA in parameter file. Perhaps a format error? Unknown keyword: 27 HP7 in parameter file. Perhaps a format error? Unknown keyword: 28 HP7 in parameter file. Perhaps a format error? Unknown keyword: 29 CGA in parameter file. Perhaps a format error? Unknown keyword: 30 O1A in parameter file. Perhaps a format error? Unknown keyword: 31 O2A in parameter file. Perhaps a format error? Unknown keyword: 32 C3A in parameter file. Perhaps a format error? Unknown keyword: 33 CMA in parameter file. Perhaps a format error? Unknown keyword: 34 HM8 in parameter file. Perhaps a format error? Unknown keyword: 35 HM8 in parameter file. Perhaps a format error? Unknown keyword: 36 HM8 in parameter file. Perhaps a format error? Unknown keyword: 37 C4A in parameter file. Perhaps a format error? Unknown keyword: 38 CHB in parameter file. Perhaps a format error? Unknown keyword: 39 HDM in parameter file. Perhaps a format error? Unknown keyword: 40 C1B in parameter file. Perhaps a format error? Unknown keyword: 41 NB in parameter file. Perhaps a format error? Unknown keyword: 42 C2B in parameter file. Perhaps a format error? Unknown keyword: 43 CMB in parameter file. Perhaps a format error? Unknown keyword: 44 HM1 in parameter file. Perhaps a format error? Unknown keyword: 45 HM1 in parameter file. Perhaps a format error? Unknown keyword: 46 HM1 in parameter file. Perhaps a format error? Unknown keyword: 47 C3B in parameter file. Perhaps a format error? Unknown keyword: 48 CAB in parameter file. Perhaps a format error? Unknown keyword: 49 HV2 in parameter file. Perhaps a format error? Unknown keyword: 50 CBB in parameter file. Perhaps a format error? Unknown keyword: 51 HVC in parameter file. Perhaps a format error? Unknown keyword: 52 HVT in parameter file. Perhaps a format error? Unknown keyword: 53 C4B in parameter file. Perhaps a format error? Unknown keyword: 54 CHC in parameter file. Perhaps a format error? Unknown keyword: 55 HAM in parameter file. Perhaps a format error? Unknown keyword: 56 C1C in parameter file. Perhaps a format error? Unknown keyword: 57 NC in parameter file. Perhaps a format error? Unknown keyword: 58 C2C in parameter file. Perhaps a format error? Unknown keyword: 59 CMC in parameter file. Perhaps a format error? Unknown keyword: 60 HM3 in parameter file. Perhaps a format error? Unknown keyword: 61 HM3 in parameter file. Perhaps a format error? Unknown keyword: 62 HM3 in parameter file. Perhaps a format error? Unknown keyword: 63 C3C in parameter file. Perhaps a format error? Unknown keyword: 64 CAC in parameter file. Perhaps a format error? Unknown keyword: 65 HV4 in parameter file. Perhaps a format error? Unknown keyword: 66 CBC in parameter file. Perhaps a format error? Unknown keyword: 67 HVC in parameter file. Perhaps a format error? Unknown keyword: 68 HVT in parameter file. Perhaps a format error? Unknown keyword: 69 C4C in parameter file. Perhaps a format error? Unknown keyword: 70 CHD in parameter file. Perhaps a format error? Unknown keyword: 71 HBM in parameter file. Perhaps a format error? Unknown keyword: 72 C1D in parameter file. Perhaps a format error? Unknown keyword: 73 ND in parameter file. Perhaps a format error? Unknown keyword: 74 C2D in parameter file. Perhaps a format error? Unknown keyword: 75 CMD in parameter file. Perhaps a format error? Unknown keyword: 76 HM5 in parameter file. Perhaps a format error? Unknown keyword: 77 HM5 in parameter file. Perhaps a format error? Unknown keyword: 78 HM5 in parameter file. Perhaps a format error? Unknown keyword: 79 C3D in parameter file. Perhaps a format error? Unknown keyword: 80 C4D in parameter file. Perhaps a format error? Unknown keyword: 81 CHA in parameter file. Perhaps a format error? Unknown keyword: 82 HGM in parameter file. Perhaps a format error? Unknown keyword: 83 CAD in parameter file. Perhaps a format error? Unknown keyword: 84 HP6 in parameter file. Perhaps a format error? Unknown keyword: 85 HP6 in parameter file. Perhaps a format error? Unknown keyword: 86 CBD in parameter file. Perhaps a format error? Unknown keyword: 87 HP6 in parameter file. Perhaps a format error? Unknown keyword: 88 HP6 in parameter file. Perhaps a format error? Unknown keyword: 89 CGD in parameter file. Perhaps a format error? Unknown keyword: 90 O1D in parameter file. Perhaps a format error? Unknown keyword: 91 O2D in parameter file. Perhaps a format error? Unknown keyword: in parameter file. Perhaps a format error? Unknown keyword: LOOP EXPL in parameter file. Perhaps a format error? in parameter file. Perhaps a format error? Unknown keyword: FE NB in parameter file. Perhaps a format error? Unknown keyword: FE NC in parameter file. Perhaps a format error? Unknown keyword: FE ND in parameter file. Perhaps a format error? in parameter file. Perhaps a format error? in parameter file. Perhaps a format error? in parameter file. Perhaps a format error? in parameter file. Perhaps a format error? Unknown keyword: in parameter file. Perhaps a format error? Unknown keyword: NB C1B in parameter file. Perhaps a format error? Unknown keyword: NC C1C in parameter file. Perhaps a format error? Unknown keyword: ND C1D in parameter file. Perhaps a format error? Unknown keyword: C1A C2A in parameter file. Perhaps a format error? Unknown keyword: C1B C2B in parameter file. Perhaps a format error? Unknown keyword: C1C C2C in parameter file. Perhaps a format error? Unknown keyword: C1D C2D in parameter file. Perhaps a format error? Unknown keyword: C2A C3A in parameter file. Perhaps a format error? Unknown keyword: C2B C3B in parameter file. Perhaps a format error? Unknown keyword: C2C C3C in parameter file. Perhaps a format error? Unknown keyword: C2D C3D in parameter file. Perhaps a format error? Unknown keyword: C3A C4A in parameter file. Perhaps a format error? Unknown keyword: C3B C4B in parameter file. Perhaps a format error? Unknown keyword: C3C C4C in parameter file. Perhaps a format error? Unknown keyword: C3D C4D in parameter file. Perhaps a format error? Unknown keyword: C4A NA in parameter file. Perhaps a format error? Unknown keyword: C4B NB in parameter file. Perhaps a format error? Unknown keyword: C4C NC in parameter file. Perhaps a format error? Unknown keyword: C4D ND in parameter file. Perhaps a format error? Unknown keyword: in parameter file. Perhaps a format error? Unknown keyword: CHARGE in parameter file. Perhaps a format error? Unknown keyword: 0.2500 in parameter file. Perhaps a format error? Unknown keyword: 0.1000 in parameter file. Perhaps a format error? Unknown keyword: 0.3000 in parameter file. Perhaps a format error? Unknown keyword: 0.0750 in parameter file. Perhaps a format error? Unknown keyword: 0.1500 in parameter file. Perhaps a format error? Unknown keyword: 0.0750 in parameter file. Perhaps a format error? Unknown keyword: 0.1500 in parameter file. Perhaps a format error? Unknown keyword: -0.1100 in parameter file. Perhaps a format error? Unknown keyword: -0.2650 in parameter file. Perhaps a format error? Unknown keyword: -0.1200 in parameter file. Perhaps a format error? Unknown keyword: 0.0200 in parameter file. Perhaps a format error? Unknown keyword: 0.0200 in parameter file. Perhaps a format error? Unknown keyword: -0.0200 in parameter file. Perhaps a format error? Unknown keyword: 0.1000 in parameter file. Perhaps a format error? Unknown keyword: 0.3000 in parameter file. Perhaps a format error? Unknown keyword: in parameter file. Perhaps a format error? Unknown keyword: DONE in parameter file. Perhaps a format error? Unknown keyword: STOP in parameter file. Perhaps a format error? >