#This example will update the bonded parameters in parameter file,including [bondtypes],[angletypes] and [dihedraltypes]; and update charges in [atoms] under the [ moleculetype ] section.
#
#Step1:
#prepare the template top files and protocols for update.

#Step2:
#Use the fitted .off file update the template files.
#Update can be done by following steps:

#a) update nonbonded parameters.
#If the number of nonbonded terms are different for every generation fitting, you need to update the nonbonded list for [ nonbond_params ] first.
# For this example, we only keep the ones for water interactions in the template file, and create the list for Ala based on .off file.
off2top protocol.nonboned_list  intra.off  template_nonbonded_ala7_water.itp nonbond.itp > out.nonbond

#b) generate the tabulated potentials based on the terms in [ nonbond_params ] section and .off file.
off2tab protocol.tab  intra.off  nonbond.itp > out.tab

#c) update the bonded parameters in parameter file, including [bondtypes],[angletypes] and [dihedraltypes].
off2top proto.bonded  intra.off template_bonded.itp  bonded.itp >out.bonded

#d)update charges in [atoms] under [moleculetype], 
off2top  proto.mol.7  intra.off  template_ala7.itp  molala7.itp > out.mol7

