#
# Generated by PyRED version SEP-2015
#     http://q4md-forcefieldtools.org
#
logfile q4md-forcefieldtools.log

# Web site: http://ambermd.org/doc6/html/AMBER-sh-5.9.html#sh-5.9.8
alias q quit
alias e edit
alias c charge

# Web site: http://ambermd.org/doc6/html/AMBER-sh-5.9.html#sh-5.9.73
verbosity 2

# Web site: http://ambermd.org/doc6/html/AMBER-sh-5.9.html#sh-5.9.2
addAtomTypes {
         { "CA"  "C"   "sp2" }
         { "CB"  "C"   "sp2" }
         { "CM"  "C"   "sp2" }
         { "CT"  "C"   "sp3" }
         { "H1"  "H"   "sp3" }
         { "H4"  "H"   "sp3" }
         { "HA"  "H"   "sp3" }
         { "HO"  "H"   "sp3" }
         { "OH"  "O"   "sp3" }
         { "OS"  "O"   "sp3" }
}

# To force the correspondance between residue names
# PDB file versus force field libraries:
# Web site: http://ambermd.org/doc6/html/AMBER-sh-5.9.html#sh-5.9.7
# addPdbResMap {
#         { 0 ALA NALA } { 1 ALA CALA }
#         { ADE DADE }
# }

# Web site: http://ambermd.org/doc6/html/AMBER-sh-5.9.html#sh-5.9.41
frcmod1 = loadAmberParams ./frcmod.known
frcmod2 = loadAmberParams ./frcmod.correspondence
# frcmod3 = loadAmberParams ./frcmod.unknown

# Web site: http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
# Web site: http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
UNK = loadmol3 Mol-sm_m1-c1.mol2

# To match the residue names found in the PDB file
# Web site: http://ambermd.org/doc6/html/AMBER-sh-5.9.html#sh-5.9.19
#ZZZ = copy UNK

# If a copy is done, define the molecule and residue
# Web site: http://ambermd.org/doc6/html/AMBER-sh-5.9.html#sh-5.9.63
#set ZZZ name "ZZZ"
#set ZZZ.1 name "ZZZ"

# Let's load the PDB file
# Web site: http://ambermd.org/doc6/html/AMBER-sh-5.9.html#sh-5.9.44
#VAR = loadPdb Mol-sm_m1-c1.pdb

# Let's save the prmtop and prmcrd file with specific file extensions
#  (to be automatically recognized by VMD http://www.ks.uiuc.edu/Research/vmd/)
# Web site: http://ambermd.org/doc6/html/AMBER-sh-5.9.html#sh-5.9.54
saveAmberParm UNK UNK.parm UNK.rst

# q