Hello, Charles,
As you suggested, I use the Python script to do my structure
calculation. I have loaded DAP residue and the peptide bond between CG of
ASP and NZ of DAP. The final structure looks reasonable except the peptide
bond between CG of ASP and NZ of DAP. The CG and NZ may not close enough
and OG CG NZ HZ atoms are not in one plane. I think I still define the
peptide somewhere, do you have any suggestion?
I have attached the script I used for calculation and the calculated
pdb file.
Thanks!
Xiaogang
On Thu, May 21, 2015 at 11:02 PM, Charles Schwieters <[email protected]
> wrote:
>
> Hello Xiaogang--
>
> >
> > I try to do structure calculation of this cyclic peptide use
> > the attached "random.inp" file which I modified from the same file
> > of 'xplor-nih/tutorial/nmr' folder. I found that in the calculated
> > PDB files, the atoms of DAP residue may get too close to each other
> > which impede the formation of the right bond topology, and the
> > peptide bond between CG of ASP and NZ of DAP are easily broken ( as
> > in the pdb file attached). I guess I need to define the DAP residue
> > and CG-NZ peptide bond somewhere before the structure
> > calculation. Do you have any suggestion about this?
> >
>
> Do you load parameters for DAP? This needs to be done, as it is in the
> gen.py file I sent you. Also, I strongly suggest that you stick with
> the Python interface, as it is simpler and has many more features. A
> good starting point is in the gb1_simple subdirectory of the hands-on
> tutorial available from
>
> http://nmr.cit.nih.gov/xplor-nih/doc/current/
>
> best regards--
> Charles
>
anneal_nordc_4.pdb
Description: Protein Databank data
anneal_nordc.py
Description: application/chimera
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