ssh bybaker@guanine.12% setenv AMBERHOME /usr/local/amber7
guanine.13% $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.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
> loadamberparams FAD4.parm
Loading parameters: ./FAD4.parm
Reading force field mod type file (frcmod)
> test = loadpdb FAD4.pdb
Loading PDB file: ./FAD4.pdb
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>
  total atoms in file: 53
  Leap added 2 missing atoms according to residue templates:
       2 Heavy
  The file contained 3 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>
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.
Failed to generate parameters
Parameter file was not saved.

guanine.3% antechamber -i FAD5.pdb -fi pdb -o FAD5.prep -fo prepi
Floating exception (core dumped)
guanine.4% rm core
rm: remove core? y
guanine.5% antechamber -i FAD4.pdb -fi pdb -o FAD5.prep -fo prepi

guanine.6% parmchk -i FAD5.prep -f prepi -o FAD5.frcmod'
guanine.6% parmchk -i FAD5.prep -f prepi -o FAD5.frcmod
guanine.7%