Dear all
I have a question regarding adding a ligand to my model. I'm not quite
sure how to do it. I have obtained the ligand in two different ways,
either in SMILES format from the drugbank or in PDB format. I have moved
the ligand into the density in coot simply by using translate and rotate
functions and then refining it to the density and merging the ligand
file with my pdb file (is this the correct way of doing this?) I know
Arpwarp ligand could be used but I have been battling to get arpwarp to
interface with ccp4 so failing using arpwarp how would one add a ligand
to a model?
Also, refmac gives me the following warning: WARNING : residue: GTX
0 chain:CC
different element name: file:"HS " dict:"H
or
ERROR : DUM : duplicated atom_name : "DUM ".
chain: CC residue: 1
Depending on which ligand I use, I do not know how to fix this, any help
would be appreciated
Thanks
Sylvia
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