Hi Sze Yi, There is already a compound named LIG in the Refmac dictionary. So either you have to choose a new name or you overrule the dictionary by supplying a restraint file in your Refmac run.
Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Lau Sze Yi (SIgN) > Sent: Monday, June 08, 2015 12:00 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Refmac fatal error with newly added ligand > > Hello, > > I generated my new ligand using smiles string in Phenix with elbow to > generate my ligand cif and pdb file. I then open these in Coot along with my > protein model and mtz and fitted this new ligand into my density. > However Refmac failed with the following details in my log file: > > PDB_code:4F80 > PDB_name:IMMUNE SYSTEM > PDB_date:16-MAY-12 > -------------------------------- > ERROR : atom :C01 LIG 1 EE is absent in the library > ERROR : atom :C02 LIG 1 EE is absent in the library > ERROR : atom :C03 LIG 1 EE is absent in the library > ERROR : atom :C04 LIG 1 EE is absent in the library > ERROR : atom :C05 LIG 1 EE is absent in the library > ERROR : atom :O06 LIG 1 EE is absent in the library > ERROR : atom :P07 LIG 1 EE is absent in the library > ERROR : atom :O08 LIG 1 EE is absent in the library > ERROR : atom :O09 LIG 1 EE is absent in the library > ERROR : atom :O10 LIG 1 EE is absent in the library > ATTENTION: atom:C28 LIG 1 EE is missing in the structure > ATTENTION: atom:C26 LIG 1 EE is missing in the structure > ATTENTION: atom:C24 LIG 1 EE is missing in the structure > ATTENTION: atom:C22 LIG 1 EE is missing in the structure > ATTENTION: atom:C21 LIG 1 EE is missing in the structure > ATTENTION: atom:C4 LIG 1 EE is missing in the structure > ATTENTION: atom:N3 LIG 1 EE is missing in the structure > ATTENTION: atom:C20 LIG 1 EE is missing in the structure > ATTENTION: atom:C17 LIG 1 EE is missing in the structure > ATTENTION: atom:C5 LIG 1 EE is missing in the structure > ATTENTION: atom:C6 LIG 1 EE is missing in the structure > ATTENTION: atom:N1 LIG 1 EE is missing in the structure > ATTENTION: atom:C7 LIG 1 EE is missing in the structure > ATTENTION: atom:C15 LIG 1 EE is missing in the structure > ATTENTION: atom:C13 LIG 1 EE is missing in the structure > ATTENTION: atom:N12 LIG 1 EE is missing in the structure > ATTENTION: atom:C10 LIG 1 EE is missing in the structure > ATTENTION: atom:C8 LIG 1 EE is missing in the structure > Number of chains : 5 > Total number of monomers : 217 > Number of atoms : 2162 > Number of missing atoms : 18 > Number of rebuilt atoms : 908 > Number of unknown atoms : 10 > Number of deleted atoms : 0 > IERR = 1 > > There is an error. See above > ===> Error: Fatal error. Cannot continue <B><FONT COLOR="#FF0000"><!-- > SUMMARY_BEGIN--> > Refmac_5.8.0123: Fatal error. Cannot continue > Times: User: 2.1s System: 0.1s Elapsed: 0:04 > </pre> > </html> > > What went wrong? Am I missing any steps in my ligand fitting? > Appreciate your feedback. > > Regards, > Sze Yi >
