Hello, I am using modeller-ligand.py script of Modeller9v6 for generation of a ligand (FE4S4 cluster ) for my modelled protein. The co-ordinates of the FE atoms and S atoms have been generated but the connect information are missing. Is there a way that somehow the ligands co-ordinates along with the connect information can be generated by the Modeller?
regards Subarna Thakur
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On 1/3/10 10:18 PM, subarna thakur wrote: > I am using modeller-ligand.py script of Modeller9v6 for generation of a > ligand (FE4S4 cluster ) for my modelled protein. The co-ordinates of the > FE atoms and S atoms have been generated but the connect information are > missing. Is there a way that somehow the ligands co-ordinates along with > the connect information can be generated by the Modeller?
Unfortunately not - Modeller does not generate PDB CONECT records. Furthermore, for BLK residues it does not even know the internal connectivity of each ligand - it simply copies the coordinates from the template.
Ben Webb, Modeller Caretaker
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subarna thakur