Step 1: Automation of the Partitioning Schemes
Automatic fragmentation of a large molecule is desirable, because of the time-consuming and error-prone aspects associated with manual fragmentation. This implementation supports protein files in PDB or MOL2 format.
For MFCC, splitting the buried residues of the protein results in two incomplete points that require two groups of conjugated caps (‘caps’) to cap the severed valences (Figure 3). For example, if the split incomplete fragments include three amino acids, the estimated atoms in the subsystems and two caps are always >60, even for small residues, constituting a relatively large system for QM calculations. According to computational efficiency and convenience, each fragment was generated by breaking the peptide bond. Assuming that one protein contains N amino acid residues (Figure 3; N = 3), N fragments and N − 1 caps will be generated after fragmentation. First, all molecular coordinates are scanned to search the split points, after which the protein is split into N incomplete fragments; each includes one or two caps according to residue location (terminus or buried area). Splitting buried residues results in two incomplete points, which require two caps (e.g., Frag 2 in Figure 3). For residues located at termini, there is only one split point, requiring only one cap (e.g., Frags 1 and 3 in Figure 3). The caps are not only used as buffered groups for residues, but also mimic the protein’s real environment.