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Hello David-- > So I run anneal.py (2.21, eginput/gb1_rdc), get my first structure, = > anneal_0.sa: > > REMARK ------------------------------------------------------------ > REMARK summary Name Energy RMS Violations > REMARK summary total -345.53 201 > REMARK summary ANGL 39.26 0.408 0 > REMARK summary BOND 5.73 0.003 0 > REMARK summary CDIH 0.04 0.066 0 > REMARK summary COLL 34.69 > REMARK summary HBDA 2.90 0.027 8 > REMARK summary IMPR 8.12 0.348 0 > REMARK summary RAMA -625.13 > REMARK summary VDW 33.72 0 > REMARK summary jcoup 35.78 0.829 6 > REMARK summary noe 8.01 0.019 0 > REMARK summary rdc 111.35 1.005 187 > > > I run analyze.py, for the same structure I get, for analyze_0.sa: > > REMARK ------------------------------------------------------------ > REMARK summary Name Energy RMS Violations > REMARK summary total 4236.14 92 > REMARK summary ANGL 39.28 0.408 0 > REMARK summary BOND 6.00 0.003 0 > REMARK summary CDIH 4454.34 22.378 4 > REMARK summary HBDA 2.91 0.027 8 > REMARK summary IMPR 8.30 0.352 0 > REMARK summary RAMA -625.02 > REMARK summary VDW -247.82 0 > REMARK summary Vgyr 0.25 0.501 0 > REMARK summary jcoup 35.76 0.829 6 > REMARK summary noe 8.01 0.019 0 > REMARK summary rdc 554.14 1.002 74 > I'm replying to the list as this is a common problem. By default, protocol.initCoords will now change atomic coordinates such that all symmetric sidechains have values in ``standard'' (mostly IUPAC) ranges. Apparently, this change is imcompatible with your dihedral restraint table. To prevent initCoords from doing this, add the option correctSymmetricSidechains=False when calling that function. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFJhz8/PK2zrJwS/lYRAi4dAJ0fZjTXF+4qiNcLP/bV1VayF0dkGgCfb3Bf Zta+z3tHV785IyyrKTTDWA0= =Gwq+ -----END PGP SIGNATURE-----
