Algorithms for calculating excluded volume and its derivatives as a function of molecular conformation and their use in energy minimization
✍ Scribed by Craig E. Kundrot; Jay W. Ponder; Frederic M. Richards
- Publisher
- John Wiley and Sons
- Year
- 1991
- Tongue
- English
- Weight
- 713 KB
- Volume
- 12
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
Abstract
A numerical method for calculating the volume of a macromolecule and its first and second derivatives as a function of atomic coordinates is presented. For N atoms, the method requires about 0.3 N ln(N) seconds of CPU time on a VAX‐8800 to evaluate the volume and derivatives. As a test case, the method was used to evaluate a pressure‐volume energy term in energy minimizations of the protein lysozyme at 1000 atm (1 atm = 1.013 × 10^5^ Pa). R.m.s. gradients of 10^−4^ kcal/mol/Å were obtained at convergence. The calculated structures exhibited pressure‐induced changes which were qualitatively similar to the changes observed in the 1000 atm structure determined by X‐ray crystallography.