Dear XPLOR users, I need to modify cysteines in my peptide pdb with IAP nitroxide spin label. I have generated so far conventional .psf and extended .pdb files for my peptide to start minimization of structure with constraints. Making non conventional .psf and .pdb files as well as modifying folded (not extended) structure in pdb by adding spin label or other things seems quite challenging to me. I have seen examples on making .psf and extended .pdb files with N-terminus and proline modifications to initiate structure calculation, but I can not figure out how to modify already existing pdb file with folded peptide in it...
I also do not know where can I get IAP spin label parameter file to merge it with my peptide pdb using some kind of python interface script. Any script, parameter file or advice would help me a lot! Thank you very much for help -- Best regards, Anna Kuznetsova Joanna R. Long research group University of Florida -------------- next part -------------- An HTML attachment was scrubbed... URL: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20120124/984f4532/attachment.html
