Atoms Not in Residue Templates | Computational Chemistry Resources

Occasionally while using a LEaP-based system, you’ll get errors like:

Created a new UNIT for residue: WAT sequence: 585
Created a new atom named: O within residue .R<WAT 585>
Created a new atom named: H1 within residue .R<WAT 585>
Created a new atom named: H2 within residue .R<WAT 585>
   total atoms in file 7658
   The file contained 7658 atoms not in residue templates

These occur when you didn’t source the correct leap files with the atom types you needed (leaprc.ff99SB, for example).

You can also get these errors if you have non-standard residues in your files, but you didn’t get the parameters you needed for them.

Created a new UNIT for residue: AKG sequence: 455
Created a new atom named: O1 within residue .R<AKG 455>
Created a new atom named: C1 within residue .R<AKG 455>
Created a new atom named: O2 within residue .R<AKG 455>
Created a new atom named: C1 within residue .R<AKG 455>
Created a new atom named: O3 within residue .R<AKG 455>
---
Created a new atom named: C4 within residue .R<AKG 455>
   total atoms in file 7658
   The file contained 69 atoms not in residue templates

Go back and load in the things you need–check the force field and check your non-standards. Effectively, begin the LEaP process all over again.