Dear all
I am trying to fit a small molecule ligand into a protein complex using
Coot. The data was processed to P212121, at 2.6 A. What I did was to input
a SMILES string, fit the ligand, merge the ligand into the protein molecule
using 'Merge Molecules' and save coordinates.
After fitting the ligand (now as chain O) I ran restrained refinement in
Refmac5 and the following error returns:
Input file :C:/20161226_1.1_refmac1-coot-1.pdb
------------------------------
--- LIBRARY OF MONOMERS ---
_lib_name mon_lib
_lib_version 5.44
_lib_update 30/05/14
------------------------------
NUMBER OF MONOMERS IN THE LIBRARY : 13409
with complete description : 13409
NUMBER OF MODIFICATIONS : 63
NUMBER OF LINKS : 73
I am reading libraries. Please wait.
- energy parameters
- monomer"s description (links & mod )
FORMATTED OLD file opened on unit 45
<B><FONT COLOR="#FF0000">
Logical name: ATOMSF, Filename: C:\CCP4-7\7.0\lib\data\atomsf.lib
</FONT></B>
Number of atoms : 19934
Number of residues : 2577
Number of chains : 15
I am reading library. Please wait.
mon_lib.cif
ERROR : DUM : duplicated atom_name : "DUM ".
chain: OO residue: 1
(And the error repeats itself for >100 times)
I believe it is due to the nomenclature of the ligand wherein Refmac
mistook atoms as DUM. (Also, the chain ID O was identified as OO?) In a
test run I carried out rigid body refinement and the programme finished
without issues.
Is there a way I could rectify the above problem? Thanks in advance for
your attention and input.
Kind regards
Sam Tang
Biochemistry Programme, School of Life Sciences, CUHK
