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Hello Sanaz-- > I call the script this way: seq2psf -protein -disulfide_bond 2:8 - > disulfide_bond 3:12 -amidate_cterm peptide.seq > > What I get are these errors: > %WDSUB-ERR: symbol not found: > improper CT CT CT OH $kchu > ^^^^^ > %energy-constant=-ERR: real number expected: > improper CT CT CT OH $kchu > ^^^^^ > %PATCH-ERR: angle -C +N +HN not found > %PATCH-ERR: improper +HN +N -C -CA not found > It looks like you are using a modified version of toppar/protein.par which invokes this undefined symbol. Please check for this. You might want to try your command with a stock-version of Xplor-NIH. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFJZPzNPK2zrJwS/lYRAi3RAJ4u8qNjczru10DRXO5aoU9qjiFUCwCfbPE7 LnzZOpSTl7+V+vLompI0UxY= =aSQL -----END PGP SIGNATURE-----
