What refinement program are you using? I assume cns. Ihe idea with the non-standard residue works very good, but the usual way is to PATCH the covalently linked molecule to its respective covalently bound atom in cns or xplor. So, you do not need to alter your pdb-file. Define a PRESI entry in topology file and set parameters in param file (see how it is done for standard patches in the existing top and param files).
Marius > 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 >> >> This message has been checked for viruses but the contents of an >> attachment may still contain software viruses, which could damage your >> computer system: you are advised to perform your own checks. Email >> communications with the University of Nottingham may be monitored as >> permitted by UK legislation. >> Dr.habil. Marius Schmidt Asst. Professor University of Wisconsin-Milwaukee Department of Physics Room 454 1900 E. Kenwood Blvd. Milwaukee, WI 53211 phone: +1-414-229-4338 email: [EMAIL PROTECTED] http://users.physik.tu-muenchen.de/marius/
