I have used TER to break the long bonds of a chain in my PDB

Question

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 ?

Answer 1

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.