<?xml version="1.0"?>
<sif>
  <!-- templates compatible with SMOG version: -->
  <version min="2.4.4"/>
  <OpenSMOGsettings>
    <constants>
      <!-- Note: K_coul is 1/5 of the value in most software
                 since SMOG models use reduced units. For discussion
                 on units in this model, see SMOG-ion manuscript
      -->
      <constant name="K_coul" value="27.787097"/>
      <constant name="dielectric" value="80"/>
    </constants>
  </OpenSMOGsettings>
  <!-- FUNCTION DEFINITIONS -->
  <!-- NOTE: Function definitions should only be changed if you modify the source code.-->
  <functions>
    <function name="bond_harmonic" directive="bonds"/>
    <function name="bond_type6" directive="bonds"/>
    <function name="angle_harmonic" directive="angles"/>
    <function name="dihedral_cosine" directive="dihedrals"/>
    <function name="dihedral_cosine4" directive="dihedrals"/>
    <function name="dihedral_harmonic" directive="dihedrals"/>
    <function name="contact_1" directive="pairs" exclusions="1"/>
    <function name="contact_free" directive="pairs" exclusions="0"/>
  </functions>
  <!-- HAMILTONIAN SETTINGS -->
  <settings>
    <!-- ENERGY/CONTACT GROUPS -->
    <Groups>
      <!-- NUCLEIC ENERGY GROUPS -->
      <!-- Normalized -->
      <energyGroup name="bb_n" residueType="nucleic" intraRelativeStrength="1" normalize="1"/>
      <energyGroup name="sc_n" residueType="nucleic" intraRelativeStrength="1" normalize="1"/>
      <!-- Not-Normalized -->
      <energyGroup name="pr_n" residueType="nucleic" normalize="0"/>
      <!-- AMINO ENERGY GROUPS -->
      <!-- Normalized -->
      <energyGroup name="bb_a" residueType="amino" intraRelativeStrength="1.0" normalize="1"/>
      <energyGroup name="sc_a" residueType="amino" intraRelativeStrength="0.5" normalize="1"/>
      <!-- Not-Normalized -->
      <energyGroup name="pr_a" residueType="amino" normalize="0"/>
      <energyGroup name="r_a" residueType="amino" normalize="0"/>
      <energyGroup name="pro_a" residueType="amino" normalize="0"/>
      <!-- LIGAND ENERGY GROUP -->
      <energyGroup residueType="ligand" name="pr_l" normalize="0"/>
      <!-- Global Contacts Settings -->
      <contactGroup name="c" intraRelativeStrength="1" normalize="1"/>
      <!-- Contact/Dihedral Group ratio: These are only used when normalization is turned on for energy groups-->
      <groupRatios contacts="2" dihedrals="1"/>
    </Groups>
    <dihedralNormalization dihedralCounting="1"/>
    <!-- CONTACT MAP SETTINGS -->
    <!-- NOTE: If another template is provided with the -t_contacts flag, then these settings will be ignored-->
    <Contacts method="shadow" contactDistance="6" shadowRadius="1" shadowRadiusBonded="0.5"/>
    <bondsThreshold shortBond="0.08" longBond="0.21"/>
    <anglesThreshold smallAngles="90" largeAngles="140"/>
    <contactsThreshold shortContacts="0.1"/>
  </settings>
  <!-- Custom Potential Info -->
  <CustomNonBonded 
	OpenSMOGparameters="ga1,gw1,gc1,ga2,gw2,gc2,C6,C12,C18,B1,C1,R1,B2,C2,R2,B3,C3,R3,B4,C4,R4,B5,C5,R5" 
	OpenSMOGcombrule=" none " 
	  OpenSMOGpotential="ga1*exp(-gw1*(r-gc1)^2)
	                +ga2*exp(-gw2*(r-gc2)^2)
	                +K_coul*q1*q2/dielectric*(1/r-1/r_c)
			+(1-2*select(C18,1,0))*C12*(1/r^12-1/r_c^12)
			+C18*(1/r^18-1/r_c^18)
			+B1*exp(-C1*(r-R1)^2)
			+B2*exp(-C2*(r-R2)^2)
			+B3*exp(-C3*(r-R3)^2)
			+B4*exp(-C4*(r-R4)^2)
			+B5*exp(-C5*(r-R5)^2)
			"/>
</sif>
