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:[log in to unmask]] On Behalf Of
> Lau Sze Yi (SIgN)
> Sent: Monday, June 08, 2015 12:00
> To: [log in to unmask]
> 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
>
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