guanine.1% setenv AMBERHOME /usr/local/amber7
guanine.2% parmchk -i
Usage: parmchk -i   input 
               -o   frcmod 
               -f   format (prepi, prepc, ac) 
               -p   ff parmfile
               -c   atom type correspondence file 
                    (default is ATCOR.DAT)
guanine.3% parmchk -i FAD4.prep -fi prepi -o FAD4.parm
guanine.4% parmchk -i FMN4.prep -fi prepi -o FMN4.parm
guanine.5% parmchk -i NAP4.prep -fi prepi -o NAP4.parm
guanine.6% 

guanine.3% parmchk -i FAD4.prep -fi prepi -o FAD4.parm
guanine.4% parmchk -i FMN4.prep -fi prepi -o FMN4.parm
guanine.5% parmchk -i NAP4.prep -fi prepi -o NAP4.parm
guanine.6% 
guanine.6% 
guanine.6% 
guanine.6% $AMBERHOME/exe/tleap
-I: Adding /usr/local/amber7/dat/leap/prep to search path.
-I: Adding /usr/local/amber7/dat/leap/lib to search path.
-I: Adding /usr/local/amber7/dat/leap/parm to search path.
-I: Adding /usr/local/amber7/dat/leap/cmd to search path.

Welcome to LEaP!
(no leaprc in search path)
> source leaprc.ff99
----- Source: /usr/local/amber7/dat/leap/cmd/leaprc.ff99
----- Source of /usr/local/amber7/dat/leap/cmd/leaprc.ff99 done
Log file: ./leap.log
Loading parameters: /usr/local/amber7/dat/leap/parm/parm99.dat
Loading library: /usr/local/amber7/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber7/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber7/dat/leap/lib/solvents.lib
> source leaprc.gaff
----- Source: /usr/local/amber7/dat/leap/cmd/leaprc.gaff
----- Source of /usr/local/amber7/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/local/amber7/dat/leap/parm/gaff.dat
> loadamberprep FAD4.prep
Loading Prep file: ./FAD4.prep
** This is a remark line: 'IMPROPER' atom C7M not found
** This is a remark line: 'IMPROPER' atom C8M not found
** This is a remark line: 'IMPROPER' atom N6A not found
> loadamberprep FMN4.prep
Loading Prep file: ./FMN4.prep
** This is a remark line: 'IMPROPER' atom C7M not found
** This is a remark line: 'IMPROPER' atom C8M not found
> loadamberprep NAP4.prep
Loading Prep file: ./NAP4.prep
** This is a remark line: 'IMPROPER' atom N6A not found
> loadamberparams FAD4.parm
Loading parameters: ./FAD4.parm
Reading force field mod type file (frcmod)
> loadamberparams FMN4.parm
Loading parameters: ./FMN4.parm
Reading force field mod type file (frcmod)
> loadamberparams NAP4.parm
Loading parameters: ./NAP4.parm
Reading force field mod type file (frcmod)
> test = loadpdb POR-2a2b.pdb
Loading PDB file: ./POR-2a2b.pdb
  Added missing heavy atom: .R<CSER 620>.A<OXT 12>
Created a new atom named: N6A within residue: .R<FAD 621>
Created a new atom named: C7M within residue: .R<FAD 621>
Created a new atom named: C8M within residue: .R<FAD 621>
  Added missing heavy atom: .R<FAD 621>.A<C4A 8>
  Added missing heavy atom: .R<FAD 621>.A<C5A 10>
Created a new atom named: C7M within residue: .R<FMN 622>
Created a new atom named: C8M within residue: .R<FMN 622>
Created a new atom named: N6A within residue: .R<NAP 623>
  total atoms in file: 5062
  Leap added 4820 missing atoms according to residue templates:
       3 Heavy
       4817 H / lone pairs
  The file contained 6 atoms not in residue templates
> saveAmberParm test test.prmtop test.inpcrd
Checking Unit.
WARNING: There is a bond of 16.116888 angstroms between: 
-------  .R<FAD 621>.A<N3A 49> and .R<FAD 621>.A<C4A 50>
WARNING: There is a bond of 16.770245 angstroms between: 
-------  .R<FAD 621>.A<C5A 45> and .R<FAD 621>.A<C6A 46>
WARNING: There is a bond of 14.378186 angstroms between: 
-------  .R<FAD 621>.A<N7A 44> and .R<FAD 621>.A<C5A 45>
WARNING: There is a bond of 13.779173 angstroms between: 
-------  .R<FAD 621>.A<C4A 8> and .R<FAD 621>.A<N9A 42>
WARNING: The unperturbed charge of the unit: -19.000000 is not zero.
FATAL:  Atom .R<FAD 621>.A<N6A 51> does not have a type.
FATAL:  Atom .R<FAD 621>.A<C7M 52> does not have a type.
FATAL:  Atom .R<FAD 621>.A<C8M 53> does not have a type.
FATAL:  Atom .R<FMN 622>.A<C7M 30> does not have a type.
FATAL:  Atom .R<FMN 622>.A<C8M 31> does not have a type.
FATAL:  Atom .R<NAP 623>.A<N6A 31> does not have a type.
Failed to generate parameters
Parameter file was not saved.
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