Hello Anna-- > > 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. >
Of course, the easiest way is to get the topology and parameter files from someone who has already created them. Anyone? In the absence of existing files, I can help you generate these if you send the exact structure to me. best regards-- Charles
-- Charles Schwieters email: [email protected] www: http://schwieters.org/cds phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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