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Hello YunLin-- > I am now trying to use GB model in my ensemble-based calculations. > While, I don't known how to set up some GB parameters (e.g. EPS, WEPS, > offset in 'gborn.inp') using python interface, the > protocol.initNBond() function do not have options for GB parameters. > so I wonder if there are some special python functions in xplor-nih to > set GB parameters? I haven't written any- I have not used the generalized born term (XPLOR terms GBIN or GBSE) during refinement. You should certainly consult the relevant literature: 1. Wagner, F. & Simonson, T., Implicit solvent models: combining an analytical formulation of continuum electrostatics with simple models of the hydrophobic effect. J Comp Chem (1999) 20, 322-335. 2. Still, W.C., Tempxzyk, A., Hawley, R., and Hendrickson, T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 112 (1990), 6127-6129. 3. Hawkins, G. Cramer, C., and Truhlar, D. Pairwise descreening of solute charges from a dielectric medium. Chem. Phys. Lett. 246 (1995), 122-129. 4. Schaefer, M. & Karplus, M. A comprehensive analytical treatment of continuum electrostatics. J. Phys. Chem. 100 (1996), 1578-1599. 5. Qiu D, Shenkin PS, Hollinger FP, Still WC, The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J. Phys. Chem. A 101, 3005-3014 (1997). > Besides, is it possible to use a hybrid script (set all other > parameters using python functions and then set up GB parameters using > xplor command) to start an ensemble-based calculation? > Probably, but I have not done so. Do note that it seems that the Amber force field is usually used with GB. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkr5tiAACgkQPK2zrJwS/lZAdQCfbmwqw9fCU2BeBKQti2+ceIx3 yLcAni9ti8SX2sQZ65PoE1m3N+5fiiIX =KhEz -----END PGP SIGNATURE-----
