Stochastic molecular optimization using generalized simulated annealing

✍ Scribed by Moret, M. A.; Pascutti, P. G.; Bisch, P. M.; Mundim, K. C.

• Publisher: John Wiley and Sons
• Year: 1998
• Tongue: English
• Weight: 583 KB
• Volume: 19
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/(sici)1096-987x(19980430)19:6<647::aid-jcc6>3.0.co;2-r

✦ Synopsis

We propose a stochastic optimization technique based on a Ž . generalized simulated annealing GSA method for mapping minima points of molecular conformational energy surfaces. The energy maps are obtained by Ž . coupling a classical molecular force field THOR package with a GSA procedure.

Ž . Unlike the usual molecular dynamics MD method, the method proposed in this study is force independent; that is, we obtain the optimized conformation without calculating the force, and only potential energy is involved. Therefore, we do not need to know the conformational energy gradient to arrive at equilibrium conformations. Its utility in molecular mechanics is illustrated by Ž . applying it to examples of simple molecules H O and H O and to 2 2 3 polypeptides. The results obtained for H O and H O using Tsallis 2 2 3

thermostatistics suggest that the GSA approach is faster than the other two Ž . conventional methods Boltzmann and Cauchy machines . The results for polypeptides show that pentalanine does not form a stable ␣-helix structure, probably because the number of hydrogen bonds is insufficient to maintain the helical array. On the contrary, the icoalanine molecule forms an ␣-helix structure. We obtain this structure simulating all ⌽, ⌿ pairs using only a few steps, as compared with conventional methods.