A continuum solvent model: the DISOLV program - algorithms, implementation, and validation
| Autor: | Kupervasser, Oleg, Zhabin, S. N., Martynov, Ya. B., Fedulov, K. M., Oferkin, I. F., Sulimov, A. V., Sulimov, V. B. |
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| Rok vydání: | 2011 |
| Předmět: | |
| Zdroj: | Numerical Methods and Programming, V.12, P.246-261 (2011) |
| Druh dokumentu: | Working Paper |
| Popis: | Several implicit (continuum) solvent models are considered: the Polarized Continuum Model (PCM), the Surface Generalized Born model (SGB), and the COnductor-like Screening model (COSMO) as well as their implementation in the form of the DISOLV program. The methods for solving the corresponding equations and for computing the analytic gradients are described. The analytic gradients are used for the fast local energy optimization of molecules in a solvent. An algorithm for the original smooth triangulated molecular surface construction is shortly discussed. The procedure for matching the model parameters and the results of the program application to proteins and ligands with the employment of the MMFF94 force field are described. The validation results show the capability of the program to reach a good accuracy (about several tenth of kcal/mol) in the case of the solvation energy calculation for reasonable time periods at arbitrary shifts of the triangulated grid in use for such large molecules as proteins. A good agreement between the calculated and experimentally measured solvation energies in water is obtained with a root-mean-square deviation about 0.8 kcal/mol for several hundreds of molecules. Comment: 58 pages, English (35 pages) and Russian (23 pages) language versions |
| Databáze: | arXiv |
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