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Hello Eugene-- > > This clears up the problem with the geometric energy terms in the refine_fu= > ll.inp calculation. The resulting energies are: thanks for the feedback. > However, although the geometric energy terms are also much lower in the ref= > ine_full.py calculation, i.e., > > REMARK ------------------------------------------------------------ > REMARK summary Name Energy RMS Violations > REMARK summary total 3987.60 877 > REMARK summary ANGL 924.26 2.028 328 > REMARK summary BOND 215.03 0.016 19 > REMARK summary CDIH 22.36 1.668 4 > REMARK summary IMPR 41.09 0.717 8 > REMARK summary NCS 280.46 > REMARK summary ORIE -598.45 > REMARK summary PLAN 39.36 , > > compared to the nucleic.top/par calculation, i.e., > > REMARK ------------------------------------------------------------ > REMARK summary Name Energy RMS Violations > REMARK summary total 77782.66 785 > REMARK summary ANGL 934.87 2.039 295 > REMARK summary BOND 252.82 0.018 23 > REMARK summary CDIH 21.94 1.652 2 > REMARK summary IMPR 76386.18 28.835 46 > REMARK summary NCS 651.75 > REMARK summary ORIE -854.54 > REMARK summary PLAN 7.04 , > > The number of experimental violations is still quite large, and the G24-C1 = > and G12-C13 base interactions are still distorted. > I'm curious: do you get the same results when you start with startB.pdb? thanks-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkt8TvoACgkQPK2zrJwS/lZxrwCfdF4UIcN3dr7z4K14SsJHmHLR pMwAoIQF389mO8DthHE5hMiVdbO6QTLJ =9hw5 -----END PGP SIGNATURE-----
