• molecular fractionation with conjugate caps (MFCC);
  • quantum mechanical computation;
  • interaction energy


We present a systematic study of numerical accuracy of various forms of molecular caps that are employed in a recently developed molecular fractionation scheme for full quantum mechanical computation of protein–molecule interaction energy. A previously studied pentapeptide (Gly-Ser-Ala-Asp-Val) or P5 interacting with a water molecule is used as a benchmark system for numerical testing. One-dimensional potential energy curves are generated for a number of peptide–water interaction pathways. Our study shows that various forms of caps all give consistently accurate energies compared to the corresponding full system calculation with only small deviations. We also tested the accuracy of cutting peptide backbone at different positions and comparisons of results are presented. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1846–1852, 2003