text: user-1: I’m now not sure what I need to alter in my PDB to get it to work in leap. I know breaking the bonds turns the formerly connected residues into terminal residues.
  It keeps saying that 3 of my atoms no longer have a type , how can I fix this ?
  
  user6322: Normally you have three options in a PDB:
  
  Add a TER record
  Add the  OXT atom, if your chain was cleaved or cleaved spontaneously (i.e. Asp-Pro sequence), the C-terminal would sill have a terminal oxygen. i.e. making it a terminal residue. If you have protons, you'll need to add also 3H .
  Assign a different chain
  
  If you are using forcefields as is your case, the second is the only choice. The C  atom and the N  atoms have a type that does not match because they have the wrong number of bonds —hence the type error.
  
original_text: -1: <p>I’m now not sure what I need to alter in my PDB to get it to work in leap. I know breaking the bonds turns the formerly connected residues into terminal residues.
  It keeps saying that 3 of my atoms no longer have a type , how can I fix this ?</p>
   6322: <p>Normally you have three options in a PDB:</p>
  <ul>
  <li>Add a <code>TER</code> record</li>
  <li>Add the <code> OXT</code> atom, if your chain was cleaved or cleaved spontaneously (<em>i.e.</em> Asp-Pro sequence), the C-terminal would sill have a terminal oxygen. i.e. making it a terminal residue. If you have protons, you'll need to add also <code>3H </code>.</li>
  <li>Assign a different chain</li>
  </ul>
  <p>If you are using forcefields as is your case, the second is the only choice. The <code>C </code> atom and the <code>N </code> atoms have a type that does not match because they have the wrong number of bonds —hence the type error.</p>
  