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Hello Fred-- > I have added hydroxyproline parameters to the protein.par and > protein.top files and have added 'HYP' to the residue types in > psfGen.py > When I use seq2psf I get the following errors: > > %PATCH-ERR: angle -C +N +HN not found > %PATCH-ERR: improper +HN +N -C -CA not found > > The program still creates the PSF file, but I was curious as to the > patch-err. > The HYP residue type is defined in the opls topology file. This file does not follow Xplor-NIH atom naming conventions. In particular, the HN atom is named H. The result here is that a peptide angle and improper are missing in your psf. One solution would be to rename the H atom to HN. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFI15okPK2zrJwS/lYRAlQPAJwLDYh1v5MWykRXDDiNQPfeMyy5mwCffkKz FWQ3HcvWZ3v/GwSuZiUmWn4= =DDge -----END PGP SIGNATURE-----
