farm@farm01:~/mirror/users/ajid/s58_kristal/complex$ tleap -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB -I: Adding /home/farm/mirror/Programs/amber/amber11/dat/leap/prep to search path. -I: Adding /home/farm/mirror/Programs/amber/amber11/dat/leap/lib to search path. -I: Adding /home/farm/mirror/Programs/amber/amber11/dat/leap/parm to search path. -I: Adding /home/farm/mirror/Programs/amber/amber11/dat/leap/cmd to search path. -f: Source /home/farm/mirror/Programs/amber/amber11/dat/leap/cmd/leaprc.ff99SB. Welcome to LEaP! (no leaprc in search path) Sourcing: /home/farm/mirror/Programs/amber/amber11/dat/leap/cmd/leaprc.ff99SB Log file: ./leap.log Loading parameters: /home/farm/mirror/Programs/amber/amber11/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/farm/mirror/Programs/amber/amber11/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) Loading library: /home/farm/mirror/Programs/amber/amber11/dat/leap/lib/all_nucleic94.lib Loading library: /home/farm/mirror/Programs/amber/amber11/dat/leap/lib/all_amino94.lib Loading library: /home/farm/mirror/Programs/amber/amber11/dat/leap/lib/all_aminoct94.lib Loading library: /home/farm/mirror/Programs/amber/amber11/dat/leap/lib/all_aminont94.lib Loading library: /home/farm/mirror/Programs/amber/amber11/dat/leap/lib/ions94.lib Loading library: /home/farm/mirror/Programs/amber/amber11/dat/leap/lib/solvents.lib > source leaprc.gaff ----- Source: /home/farm/mirror/Programs/amber/amber11/dat/leap/cmd/leaprc.gaff ----- Source of /home/farm/mirror/Programs/amber/amber11/dat/leap/cmd/leaprc.gaff done Log file: ./leap.log Loading parameters: /home/farm/mirror/Programs/amber/amber11/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.4, March 2010) add. info. at the end > loadamberparams s58k.frcmod Loading parameters: ./s58k.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > loadoff s58k.lib Loading library: ./s58k.lib > 6COXAs58 = loadpdb 6COXS.pdb Loading PDB file: ./6COXS.pdb Added missing heavy atom: .R.A total atoms in file: 4499 Leap added 4403 missing atoms according to residue templates: 1 Heavy 4402 H / lone pairs > saveamberparm 6COXAs58 6COXAvakum.prmtop 6COXAvakum.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: -3.001000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Could not find bond parameter for: SH - SH Could not find bond parameter for: SH - SH Could not find bond parameter for: SH - SH Could not find bond parameter for: SH - SH Could not find bond parameter for: SH - SH Building angle parameters. Could not find angle parameter: HS - SH - SH Could not find angle parameter: SH - SH - CT Could not find angle parameter: SH - SH - HS Could not find angle parameter: CT - SH - SH Could not find angle parameter: HS - SH - SH Could not find angle parameter: SH - SH - CT Could not find angle parameter: SH - SH - HS Could not find angle parameter: CT - SH - SH Could not find angle parameter: HS - SH - SH Could not find angle parameter: SH - SH - CT Could not find angle parameter: SH - SH - HS Could not find angle parameter: CT - SH - SH Could not find angle parameter: HS - SH - SH Could not find angle parameter: SH - SH - CT Could not find angle parameter: SH - SH - HS Could not find angle parameter: CT - SH - SH Could not find angle parameter: HS - SH - SH Could not find angle parameter: SH - SH - CT Could not find angle parameter: SH - SH - HS Could not find angle parameter: CT - SH - SH Building proper torsion parameters. ** No torsion terms for HS-SH-SH-CT ** No torsion terms for HS-SH-SH-HS ** No torsion terms for CT-SH-SH-CT ** No torsion terms for CT-SH-SH-HS ** No torsion terms for HS-SH-SH-CT ** No torsion terms for HS-SH-SH-HS ** No torsion terms for CT-SH-SH-CT ** No torsion terms for CT-SH-SH-HS ** No torsion terms for HS-SH-SH-CT ** No torsion terms for HS-SH-SH-HS ** No torsion terms for CT-SH-SH-CT ** No torsion terms for CT-SH-SH-HS ** No torsion terms for HS-SH-SH-CT ** No torsion terms for HS-SH-SH-HS ** No torsion terms for CT-SH-SH-CT ** No torsion terms for CT-SH-SH-HS ** No torsion terms for HS-SH-SH-CT ** No torsion terms for HS-SH-SH-HS ** No torsion terms for CT-SH-SH-CT ** No torsion terms for CT-SH-SH-HS Building improper torsion parameters. total 1866 improper torsions applied Building H-Bond parameters. Parameter file was not saved. > quit