<?xml version="1.0"?>
<sif>
  <!-- templates compatible with SMOG version: -->
  <version min="2.3"/>
  <!-- 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_harmonic" directive="dihedrals"/>
    <function name="contact_1" directive="pairs" exclusions="1"/>
  </functions>
  <!-- HAMILTONIAN SETTINGS -->
  <settings>
    <!-- ENERGY/CONTACT GROUPS -->
    <Groups>
      <!-- NUCLEIC ENERGY GROUPS -->
      <!-- Normalized: bb=back bone, sc=side chain-->
      <energyGroup name="bb_n" residueType="nucleic" intraRelativeStrength="1.0" normalize="1"/>
      <energyGroup name="sc_n" residueType="nucleic" intraRelativeStrength="1.0" normalize="1"/>
      <!-- Not-Normalized: planar rigid dihedrals -->
      <energyGroup name="pr_n" residueType="nucleic" normalize="0"/>
      <!-- AMINO ENERGY GROUPS -->
      <!-- Normalized: bb=back bone, sc=side chain -->
      <energyGroup name="bb_a" residueType="amino" intraRelativeStrength="1.0" normalize="1"/>
      <energyGroup name="sc_a" residueType="amino" intraRelativeStrength="0.5" normalize="1"/>
      <!-- Not-Normalized: pr=planar rigid, pro= rigid proline ring, r= rigid-->
      <energyGroup name="pr_a" residueType="amino" normalize="0"/>
      <energyGroup name="pro_a" residueType="amino" normalize="0"/>
      <energyGroup name="r_a" residueType="amino" normalize="0"/>
      <!-- LIGAND ENERGY GROUP -->
      <energyGroup name="bb_l" residueType="ligand" normalize="1" intraRelativeStrength="1.0"/>
      <energyGroup name="r_l" residueType="ligand" 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="0.2"/>
    <anglesThreshold smallAngles="90" largeAngles="140"/>
    <contactsThreshold shortContacts="0.1"/>
  </settings>
</sif>
