Info: FragIt [CONFIG] reading config from 'myconfig.ini':

   Contents of the config file
 -------------------------------
[mergepatterns]
glycine = 

[fragmentation]
chargemodel = MMFF94
combinefragments = 
writer = GAMESS-FMO
groupcount = 1
maxfragsize = 100

[explicitfragmentpairs]
pairs = 

[mfcc]
order = 0

[fragmentpatterns]
a-d-pyranose = [$(C1C(CO)OC(O)C(O)C1(O))][$(OC1C(O)C(O)CC(CO)O1)]
peptide = [$(CN)][$(C(=O)NCC(=O))]
dnabackbone = [$(CCOP)][$(CC1OCCC1)]

[qmmm]
includecovalent = False
includeallwithin = 0.0
hbonddistancemin = 2.5
hbondangle = 110.0
hbonddistancemax = 3.9
includehbondacceptors = False
includehbonddonors = False

[fmo]
dohop = False
efpwaters = 0

[protectpatterns]
nterminal = [$([NH2]),$([NH3])]CC(=O)[$(NCC=O)]

[explicitprotectatoms]
atomids = 

[output]
freezebackbone = False
verbose = True
useatomnames = False
buffer = 0.0
writejmol = True
boundaries = 
writepymol = True
centralfragment = 0
active = 0.0

[qm]
basis = 3-21G


 -------------------------------
Info: FragIt [FRAGMENTATION] will break the following bonds defined in config file:


      Searching for 'a-d-pyranose' bonds.
      Pattern: '[$(C1C(CO)OC(O)C(O)C1(O))][$(OC1C(O)C(O)CC(CO)O1)]'
      Found 0 matching bonds.

      Searching for 'peptide' bonds.
      Pattern: '[$(CN)][$(C(=O)NCC(=O))]'
      Found 8 matching bonds.
      bond pair           (2,3) will not be broken.

      Searching for 'dnabackbone' bonds.
      Pattern: '[$(CCOP)][$(CC1OCCC1)]'
      Found 0 matching bonds.
Info: FragIt [CONFIG] reading config from 'myconfig.ini':

   Contents of the config file
 -------------------------------
[mergepatterns]
glycine = 

[fragmentation]
chargemodel = MMFF94
combinefragments = 
writer = GAMESS-FMO
groupcount = 1
maxfragsize = 100

[explicitfragmentpairs]
pairs = 

[mfcc]
order = 0

[fragmentpatterns]
a-d-pyranose = [$(C1C(CO)OC(O)C(O)C1(O))][$(OC1C(O)C(O)CC(CO)O1)]
peptide = [$(CN)][$(C(=O)NCC(=O))]
dnabackbone = [$(CCOP)][$(CC1OCCC1)]

[qmmm]
includecovalent = False
includeallwithin = 0.0
hbonddistancemin = 2.5
hbondangle = 110.0
hbonddistancemax = 3.9
includehbondacceptors = False
includehbonddonors = False

[fmo]
dohop = False
efpwaters = 0

[protectpatterns]
nterminal = [$([NH2]),$([NH3])]CC(=O)[$(NCC=O)]

[explicitprotectatoms]
atomids = 

[output]
freezebackbone = False
verbose = True
useatomnames = False
buffer = 0.0
writejmol = True
boundaries = 
writepymol = True
centralfragment = 0
active = 0.0

[qm]
basis = 3-21G


 -------------------------------
Info: FragIt [FRAGMENTATION] will break the following bonds defined in config file:


      Searching for 'a-d-pyranose' bonds.
      Pattern: '[$(C1C(CO)OC(O)C(O)C1(O))][$(OC1C(O)C(O)CC(CO)O1)]'
      Found 0 matching bonds.

      Searching for 'peptide' bonds.
      Pattern: '[$(CN)][$(C(=O)NCC(=O))]'
      Found 8 matching bonds.
      bond pair           (2,3) will not be broken.

      Searching for 'dnabackbone' bonds.
      Pattern: '[$(CCOP)][$(CC1OCCC1)]'
      Found 0 matching bonds.