This module is for automatically preparation of Amber force-field parameters for protein–peptide systems, including those containing non-canonical amino acids (NCAAs) and multiple complicated cyclisations. Simply upload a prepared pdb file with explicit hydrogen atoms, the workflow will detect all NCAAs and list them under the Browse button. The non-backbone connections will be automatically detected, which is used for deriving buiding blocks with NME/ACE caps. The formal and partial charges of these blocks will then be estimated via a QM-based RESP/BCC charge-fitting procedure. Since the lower letters will be used inside the workflow, it is strongly recommend to avoid using any lower-case letters in residue names. After the job finished, you can download the MD ready parameter files in the user center.

2026-07-12 update: non-standard capping fully suportted for BCC charge scheme and non-standard DNA/RNA residues