[amehta@master 3I8X]$ tleap -f oldff/leaprc.ff99SB
-I: Adding /home/amehta/amber14/dat/leap/prep to search path.
-I: Adding /home/amehta/amber14/dat/leap/lib to search path.
-I: Adding /home/amehta/amber14/dat/leap/parm to search path.
-I: Adding /home/amehta/amber14/dat/leap/cmd to search path.
-f: Source oldff/leaprc.ff99SB.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: /home/amehta/amber14/dat/leap/cmd/oldff/leaprc.ff99SB
Log file: ./leap.log
Loading parameters: /home/amehta/amber14/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/amehta/amber14/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /home/amehta/amber14/dat/leap/lib/all_nucleic94.lib
Loading library: /home/amehta/amber14/dat/leap/lib/all_amino94.lib
Loading library: /home/amehta/amber14/dat/leap/lib/all_aminoct94.lib
Loading library: /home/amehta/amber14/dat/leap/lib/all_aminont94.lib
Loading library: /home/amehta/amber14/dat/leap/lib/ions94.lib
Loading library: /home/amehta/amber14/dat/leap/lib/solvents.lib
> loadamberprep gdp.prep
Loading Prep file: ./gdp.prep
> loadamberparams frcmod.phos
Loading parameters: ./frcmod.phos
Reading force field modification type file (frcmod)
Reading title:
#  Modifications to the AMBER94 force field for polyphosphates
> mol = loadpdb 3i8x_gdp.pdb
Loading PDB file: ./3i8x_gdp.pdb
 (starting new molecule for chain A)
 (starting new molecule for chain B)
 (starting new molecule for chain C)
-- residue 823: duplicate [ C1'] atoms (total 3)
-- residue 823: duplicate [ C2] atoms (total 3)
-- residue 823: duplicate [ C2'] atoms (total 3)
-- residue 823: duplicate [ C3'] atoms (total 3)
-- residue 823: duplicate [ C4] atoms (total 3)
-- residue 823: duplicate [ C4'] atoms (total 3)
-- residue 823: duplicate [ C5] atoms (total 3)
-- residue 823: duplicate [ C5'] atoms (total 3)
-- residue 823: duplicate [ C6] atoms (total 3)
-- residue 823: duplicate [ C8] atoms (total 3)
-- residue 823: duplicate [ N1] atoms (total 3)
-- residue 823: duplicate [ N2] atoms (total 3)
-- residue 823: duplicate [ N3] atoms (total 3)
-- residue 823: duplicate [ N7] atoms (total 3)
-- residue 823: duplicate [ N9] atoms (total 3)
-- residue 823: duplicate [ O1A] atoms (total 3)
-- residue 823: duplicate [ O1B] atoms (total 2)
-- residue 823: duplicate [ O2'] atoms (total 3)
-- residue 823: duplicate [ O2A] atoms (total 3)
-- residue 823: duplicate [ O2B] atoms (total 3)
-- residue 823: duplicate [ O3'] atoms (total 3)
-- residue 823: duplicate [ O3A] atoms (total 3)
-- residue 823: duplicate [ O3B] atoms (total 3)
-- residue 823: duplicate [ O4'] atoms (total 3)
-- residue 823: duplicate [ O5'] atoms (total 3)
-- residue 823: duplicate [ O6] atoms (total 3)
-- residue 823: duplicate [ PA] atoms (total 3)
-- residue 823: duplicate [ PB] atoms (total 3)

   Warning: Atom names in each residue should be unique.
     (Same-name atoms are handled by using the first
      occurrence and by ignoring the rest.
      Frequently duplicate atom names stem from alternate
      conformations in the PDB file.)

  total atoms in file: 6407
  Leap added 6441 missing atoms according to residue templates:
       6441 H / lone pairs
> quit
        Quit
[amehta@master 3I8X]$