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Hello Lei-- > I have been struggling in refining a protein. However, I > have problems with vdw violations. I usually ended up with around 40 > vdw violations. It is probably violated to satisfy other potentials. > I tried use all atom vdW interaction instead of CA atom only (high > vdw interaction). I also tried to increase the weight of vdW ( result > in poor sampling). Are these vdw calculations as reported by the Python scripts? These are to be taken not so seriously at this point. In fact there is a bug in Xplor-NIH 2.17 such that the vdw violations are overcounted. There's a fix for this here: http://nmr.cit.nih.gov/xplor-nih/updates/2.17/ best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFGTcRuPK2zrJwS/lYRAv4tAJ91eFJ4WokzCR4XOjJKcw0cYgMYCwCdGeTx 42VnjyhXxiCKKstSeA0l3TI= =CXyo -----END PGP SIGNATURE-----
