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Hello-- > I would like to use seq2psf to create a protein that contains > hydroxyproline (HYP). Which topology file does seq2psf use? Is there a > standard topology and paramater file that already has HYP or do I need > to add it? One approach would be to add HYP to toppar/protein.top and associated parameters to toppar/protein.par. You would also need to add HYP residueTypes['prot'] at the top of python/psfGen.py. Alternatively, you could follow the example in eginput/PSF_generation/addAtoms.py replacing CYSP (MTSL) with HYP. This is probably an easier route to get a psf. If you're not not working from a homologous protein (you have no starting structure), you can replace the lines protocol.addUnknownAtoms(dyn_stepsize=0.01) protocol.fixupCovalentGeom(sel=notKnown) with try: protocol.genExtendedStructure() except protocol.CovalentViolation: pass best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFH8owTPK2zrJwS/lYRAvy8AJ0cqxYMp+1fv1NkAyoOdlsEw8O7ewCeOR/B 7jNj3R3ho800Gv/ksMqC7fo= =7M+6 -----END PGP SIGNATURE-----
