Hello Charles,
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?
Thank you!
Xiaogang
On Tue, May 19, 2015 at 3:25 AM, Charles Schwieters <[email protected]>
wrote:
>
> Hello Xiaogang--
>
> >
> > Thank you for your advice! I wrote a script as you suggest, but it
> does not
> > work! I append it at the the end of this email, and put some comments in
> it. Can
> > you help me to check what's wrong with it?
> >
>
> Please check carefully over the attached script and its output.
>
> best regards--
> Charles
>
>
random.inp
Description: chemical/gamess-input
random_3.pdb
Description: Protein Databank data
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