Acta Crystallographica Section D

Biological Crystallography

Volume 59, Part 2 (February 2003)

Acta Cryst. (2003). D59, 274-289 [doi:10.1107/S0907444902021431]

An automatic method to generate force-field parameters for hetero-compounds

K. Nilsson, D. Lecerof, E. Sigfridsson and U. Ryde

Abstract: A program, Hess2FF, has been developed that automatically constructs parameter and topology files to be used in crystallographic refinement for any molecule, based on a Hessian (force-constant) matrix estimated by any method. The program is tested by redefining hetero-compounds in five different proteins: the inhibitor N-methylmesoporphyrin bound to ferrochelatase, the haem group and its axial ligands in cyctochrome c₅₅₃, the active-site metal ion in iron superoxide dismutase, the catalytic zinc ion in alcohol dehydrogenase with a bound trifluoroethanol molecule and the 5'-deoxyadenosyl group in methylmalonyl coenzyme A mutase. It is shown that the resulting structures are improved in several aspects. In particular, the free R_free factor always decreases and it is shown that a 1.70 Å structure of cyctochrome c₅₅₃ becomes more similar to a high-resolution (0.97 Å) structure of the same protein after re-refinement with Hess2FF. Thus, the force field used in crystallographic refinement significantly affects the final structure and therefore should be published together with the structure to ensure reproducibility. Various methods of obtaining the Hessian matrix employed by Hess2FF are discussed and some recommendations are given. Hess2FF allows the user to divide the atoms of the molecule into atom types that share the same force-field parameters. However, it seems to be favourable to assign a separate type to each atom, which can be performed automatically.

Online 24 January 2003


	Text file (3.4 kbytes) The final coordinates of MMP in ferrochelataqse, obtained with the B3LYP/C1 force field

	Text file (8.3 kbytes) The CNS topology file for the B3LYP/C1 force field for MMP

	Text file (14.7 kbytes) The CNS parameter file for the B3LYP/ce force field for MMP

	Text file (4.7 kbytes) The final coordinates of His36, Met71 and the haem group in cytochrome c553, obtained with the B3LYP/CI force field

	Text file (8.8 kbytes) The CNS topology file for the B3LYP/CI field for haem in cytochrome c553

	Text file (6.0 kbytes) The CNS parameter file for the B3LYP/CI force field for haem cytochrome c553

	Text file (4.6 kbytes) The final coordinates of Cys46, His67, Cys174, the catalytic zinc ion, and the trifluoroethanol molecule in alcohol dehydrogenase, obtained with the Hess2FF/B3LYP force field with bonds and angles

	Text file (2.3 kbytes) The CNS topology file for the B3LYP force field for the catalytic zinc ion and trifluoroethanol molecule in alcohol dehydrogenase

	Text file (2.9 kbytes) The CNS parameter file for the B3LYP force field for the catalytic zinc ion and trifluoroethanol molecule in alcohol dehydrogenase

	Text file (6.9 kbytes) The final coordinates of His-33, His84, Asp170, His174, the catalytic iron ion, and the metal-bound hydroxide ion in superoxide dismutase, obtained with the B3LYP force field with bond, angles, and dihedrals

	Text file (1.9 kbytes) The CNS topology file for the B3LYP force field of the active-site iron ion in superoxide dismutase

	Text file (6.3 kbytes) The CNS parameter file for the B3LYP force field of the active-site iron ion in superoxide dismutase

	Text file (2.9 kbytes) The final coordinates of 5'-deoxyadenosine in methylmalonyl coenzyme A mutase, obtained with the B3LYP/CI force field

	Text file (3.3 kbytes) The CNS topology file for the B3LYP/CI force field for 5'-deoxyadenosine

	Text file (2.4 kbytes) The CNS parameter file for the B3LYP/CI force field for 5'-deoxyadenosine

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