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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 ?

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  • $\begingroup$ For the rest of us could you explain leap please? $\endgroup$
    – M__
    Nov 22 '20 at 10:50
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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.

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