[Chimera-users] Question about peptide connection

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 26 14:14:07 PDT 2021

Hi Nicole,
(1) If you are adding a whole amino acid residue to the end of a peptide chain, see command "addaa."  So maybe you wouldn't need to add it one atom at a time.  However, I don't know if "addaa" would work in your specific situation where you are really in the middle of the chain instead of its very beginning or end.

(2) You would also need to add a bond to connect the two parts.  Maybe that is part of the problem... if there is no bond, extra hydrogens will be added to fill the valence(s) of the atom(s) instead.

(3) However, the Reply Log image shows that there are lots of unrecognized atom names.  See that long list of residues?   So there are lots of unrecognized names, not just in the glycine you added.  Usually unrecognized names are for hydrogen atoms, so one thing to try is to delete all hydrogens e.g. command

delete H

... and then try minimization, which will re-add hydrogens, assign charges, etc.  If that still doesn't work, then you could use menu Help... Report a Bug and attach your structure PDB file.  Make sure to include your e-mail address and a short description so we know that it's this issue we are discussing now.  Without seeing your file we can't really say for sure what was wrong with it.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 26, 2021, at 12:19 PM, Nicole Ostrovsky via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Hello,
> I have a structure which I've cut a section out of and I am working on connecting the two loose ends together. I wanted to connect them with two glycine residues - since they are easiest to work with and have no side chains. I am doing this using the Modify Structure option under the Build structure tool and adding one atom at a time. However, when I try to minimize my newly created glycine, I get the error message "No MMTK name for atom "H1" in standard residue "GLY"" (I've attached a picture of my reply log). I'm not sure how to troubleshoot this.
> Is there a better way to connect two ends of a peptide, or should I change the way I am using the modify structure tool?
> Thank you.
> Nicole Ostrovsky
> <replylog_chimera.png>

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