You need a LINK record in the PDB and a dictionary to describe the link.
If you run the job from the GUI with Review Restraints, the program
should write out a suitable dictionary to describe the link. Check the
distances etc to see if you agree with them. You then use the extended
pdb and that dictionary for subsequent refinement jobs.
Eleanor
Joe Krahn wrote:
In general, it requires a LINK record to add the required bond. I don't
know how to set up refinement parameters. I had a similar case once (see
1ECC), and created a big non-standard residue containing both the amino
acid and ligand as one residue. (But, that was done in X-PLOR.) If
setting up link paramaters become a hassle, you might try the
single-residue approach.
Joe
Hall Gareth wrote:
Dear ccp4bb users,
I am currently refining a crystal structure of a protein with a
drug molecule in the active site. The drug molecule is seen, as
expected, to covalently bind to the active site. Therefore, can anyone
tell me what I need to do to alter the pdb file so as to form a covalent
bond between the protein and my drug molecule?
Cheers in advance,
Gareth Hall
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