Atomic properties of amino acids: computed atom types as a guide for future force-field design.
The quantum chemical topology (QCT) is able to propose atom types by direct computation rather than by chemical intuition. In previous work, molecular electron densities of 20 amino acids and smaller derived molecules were partitioned into a set of 760 topological atoms. Each atom was characterised by seven atomic properties and subjected to cluster analysis element by element, that is, C, H, O, N, and S. From the respective dendrograms, 21 carbon atom types were distinguished, 7 hydrogen, 2 nitrogen, 6 oxygen, and 6 sulfur atom types. Herein, we contrast the QCT atom types with those of the assisted model building with energy refinement (AMBER) force field. We conclude that in spite of fair agreement between QCT and AMBER atom types, the latter are sometimes underdifferentiated and sometimes overdifferentiated. In summary, we suggest that QCT is a useful guide in designing new force fields or improving existing ones. The computational origin of QCT atom types makes their determination unbiased compared to atom type determination by chemical intuition and a priori assumptions. We provide a list of specific recommendations.
Popelier
Paul L
PL
Department of Chemistry, U.M.I.S.T, P.O. Box 88, Sackville Street, Manchester M60 1QD, U.K. pla@umist.ac.uk
Aicken
Fiona M
FM
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D002244:Carbon / Q000737:chemistry; D016000:Cluster Analysis; D015394:Molecular Structure; D009584:Nitrogen / Q000737:chemistry; D010100:Oxygen / Q000737:chemistry; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D012984:Software; D013455:Sulfur / Q000737:chemistry
D000596:Amino Acids; D011506:Proteins; D013455:Sulfur; D002244:Carbon; D009584:Nitrogen; D010100:Oxygen