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Hello-- > I have added hydroxyproline parameters to the protein.par and protein.top. > When I run the generate script (to get an ideal geometry pdb from the > psf) I get the error > > %CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%% > bond energy constant missing. > target bond length missing. > ATOM1: SEGId=" ", RESId="12 ", NAME="CG ", CHEMical="CP " > ATOM2: SEGId=" ", RESId="12 ", NAME="OD1 ", CHEMical="OH " > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %CODBON-ERR: program will be aborted. > This means you're missing at least one parameter in protein.par. Almost all of these parameters are specified by atom (chemical) type (CP and OH in this case). Your entry for HYP must have a bond between CG and OD1- so you'll need a corresponding bond parameter entry in protein.par. Maybe bond CP OH $kbon 1.38 Note, however, that we generally use atom type CP for CG and CD in proline, so it would be better to change the atom type. Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFH85OmPK2zrJwS/lYRAtp6AJwJsZ3HVvRYpOOCC3gDo6JpVUw56ACeKIFR 2Fa5kY0HOPmAuWL84CEXAPI= =1wbE -----END PGP SIGNATURE-----
