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Geometry optimization of Kringle 1 of plasminogen using the PM3 semiempirical method

✍ Scribed by Andrew D. Daniels; Gustavo E. Scuseria; Ödön Farkas; H. Bernhard Schlegel

Publisher
John Wiley and Sons
Year
2000
Tongue
English
Weight
212 KB
Volume
77
Category
Article
ISSN
0020-7608

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✦ Synopsis

The results of a geometry optimization on the 1226 atom Kringle 1 of plasminogen are presented. The energy and gradients were calculated using a linearscaling PM3 semiempirical method with a conjugate gradient density matrix search replacing the diagonalization step. The geometry was optimized with the rational function optimization technique combined with a modified version of the direct inversion in the iterative subspace procedure. The optimization required 362 geometry update steps to reach a local minimum. An analysis is given of the optimization and timing results using a single processor on the SGI Origin2000.

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