[phenixbb] C-ter amidation of peptide

May Marsh may at cryst.bioc.cam.ac.uk
Tue Nov 10 14:08:32 PST 2009

Hi Nate,

I had a very similar problem which I solved by first manually adding a link
record to the pdb.


LINK        N    NH2 C   6                C    ALA C   5

Then running phenix.link_edits to create a restraints file.

I hope that helps,


On Nov 9 2009, Nate Nicely wrote:

>Dear all,
> How best to handle a C-terminally amidated peptide in phenix? I defined 
> the atom as 'N' and the resname as 'NH2' following a structure I found 
> that also bears a C-terminally amidated peptide. However phenix.refine 
> seems not to be making the linkage between the amide and the preceding 
> residue. Putting the structure into phenix.elbow returns, "No unknown 
> residues."
>Nate N.
>phenixbb mailing list
>phenixbb at phenix-online.org

  Dr. May Marsh
  Department of Biochemistry, University of Cambridge
  may at cryst.bioc.cam.ac.uk
  tel:    +44-(0)1223 760 468

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