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
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--
Charles Schwieters email: Charles at Schwieters.org
www: http://schwieters.org/cds
phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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