Global energy minimization of small molecules combining Constraint Logic Programming and molecular mechanics

D. Zupanic, M. Hodoscek, N. Lavrac, and I. Mozetic. Journal of Chemical Information and Computer Sciences, 37(6):966--971, December 1997. More behind this link.

Abstract

The paper presents an approach to molecular energy minimization using Constraint Logic Programming (CLP) as a preprocessor to a molecular mechanics minimization program such as CHARMM. The use of CLP enables the definition of simple constraints that sufficiently describe relations in a molecule, thus limiting the search space of the globally optimal solution. The approach was used on the problem of minimizing the energy of the alanine dipeptide and N-methylalanylacetamide. An approximate 3-D structure produced by a CLP system was used as an initial structure for the CHARMM program that considers all relations in such a structure and performs energy optimization. With this initial structure, computed in about one minute of CPU time, the optimal solution (global minimum) was found in only few seconds, while calculating the same solution with CHARMM alone took 15 hours. All calculations were performed on HP/735.

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D. Zupanic, darko.zupanic@ijs.si,