By Oren M Becker; et al
ISBN-10: 082470455X
ISBN-13: 9780824704551
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44. D Eisenberg, AD McLachlan. Nature 319:199–203, 1986. 45. L Wesson, D Eisenberg. Protein Sci 1:227–235, 1992. 46. MK Gilson, ME Davis, BA Luty, JA McCammon. J Phys Chem 97:3591–3600, 1993. 47. M Schaefer, M Karplus. J Phys Chem 100:1578–1599, 1996. 48. M Nina, D Beglov, B Roux. J Phys Chem B 101:5239–5248, 1997. 49. D Sitkoff, KA Sharp, B Honig. J Phys Chem 98:1978–1988, 1994. 50. D Qui, PS Shenkin, FP Hollinger, WC Still. J Phys Chem A 101:3005–3014, 1997. 51. B Jayaram, D Sprous, DL Beveridge.
Care must be taken at this stage that the total charge on the molecule is zero. Alternatively, charges from Mulliken population analysis of an HF/ 6-31G* [84] calculation could act as a starting point. Concerning the VDW parameters, assignment of the appropriate types of atoms to the model compound simultaneously assigns the VDW parameters. At this point the information required by CHARMM to create the molecule is present, but the parameters necessary to perform energy calculations are not all available yet.
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Computational biochemistry and biophysics by Oren M Becker; et al
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