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AMBER force‐field parameters for guanosine triphosphate and its imido and methylene analogs
Author(s) -
Can John F.
Publication year - 1993
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540140815
Subject(s) - mndo , gtp' , guanosine , chemistry , force field (fiction) , guanosine triphosphate , atom (system on chip) , computational chemistry , crystallography , stereochemistry , molecule , physics , quantum mechanics , organic chemistry , biochemistry , computer science , embedded system , enzyme
Parameters were derived for guanosine triphosphate (GTP) and GTP analogs suitable for the AMBER force field. Electrostatically derived net atomic charges and force parameters were extracted from MNDO semiempirical calculations. The later parameters came from fitting MNDO and AMBER atom–atom forces in a manner that is extensible to other compounds that lack sufficient vibrational spectral data. The geometric parameters for these compounds were obtained from model compounds in the Cambridge crystallographic data base. Dynamic simulations of Na 4 GTP and Na 2 Mg GTP of 140 and 100 ps, respectively, indicated a strong preference for a syn C2′ exo conformation in solution. © 1993 John Wiley & Sons, Inc.