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

The results of a geometry optimization on the 1226 atom Kringle I of plasmi nogen are presented. The energy and gradients were calculated using a linea r-scaling 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 vers ion of the direct inversion in the iterative subspace procedure. The optimi zation required 362 geometry update steps to reach a local minimum. An anal ysis is given of the optimization and timing results using a single process or on the SGI Origin2000. (C) 2000 John Wiley & Sons, Inc.