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Hello Indra--
> I am trying to add MTSL paramagnetic probe in a membrane protein
> using xplor.
> I modified the addAtoms.py file with my protein sequence and my
> original structure (start.pdb) at proper places. I used CYSP as the
> MTSL probe at the desired position (as suggested in the tutorials) in
> the protein sequence. When I executed the command "xplor -py
> addAtoms.py" , it seems working and new.pdb and new.psf files are
> generated with MTSL labeled at proper position in the protein
> sequence. When I compare the new.pdb with start.pdb, it seems that
> the structure is distorted (alpha helix to random coil).
Of course, this should not happen. Are there any diagnostic messages?
> I used
> cysp.top and cysp.par as topology and parameter files.
CYSP is now included in the standard toppar input, so these additional
files should cause errors (with recent versions of Xplor-NIH).
So there must be some error messages...
best regards--
Charles
- --
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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