Phospho-serine patch

James Horne h.horne at medicine.unimelb.edu.au
Sun Jan 23 18:54:52 EST 2000


Jeannie Rojas wrote:
> 
> Hello,
> 
> I am trying to refine a phosphorylated serine residue in CNS.  I
> downloaded the topology and parameter files from the HIC-UP database.
> I attempted to incorporate these files into the generate.inp script but
> the phospho-serine residue (SEP) is still not recognized? I would
> appreciate any help.  Thanks.
> 
> ---

Dear Jeannie

I've been "Xplor-ing" with a bunch of protein kinases for some time now
that incorporate phosphoserine and phosphotyrosines in some models.  It
would be handy to see the output of some of your log files with the
errors you are getting.  I got it all to work eventually and you would
be welcome to have a copy of my own topology and parameter files which
have been edited with charges and some renaming of atom types where
appropriate.  I made sure the backbone atoms of SEP were at least given
the same name as the corresponding SER residue.  Otherwise, you get
CODBOND errors at the point before and after the SEP residue in the
peptide chain.  There may be several ways around this sort of thing but
I have working files if you would like a copy to look at.

Just let me know.

Cheers

James Horne




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