[Chimera-users] No MMTK name for atom "H" in standard residue "GLY"

[Eric Pettersen]

Hi Marco,
	Chimera assigns partial charges and atom types to the atoms of standard residues by looking up the atom name in a table.  That means that those atoms have to have their PDB standard names.  There is no atom named 'H' in a standard N-terminal glycine.  The hydrogens attached to the N should be named H1, H2, and H3, and the ones attached to the CA should be named HA1 and HA2.
	Assuming it wasn't Chimera that added this 'H', an easy way to fix it is with the commands (Favorites→Command Line) "del H" followed by "addh".  Then you should be able to minimize.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Nov 12, 2022, at 3:15 AM, Marco Sette via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear all,
> 
> i'm trying to minimize a peptide (Tools, Structure editing, Minimize Structure) but I obtain this error message: No MMTK name for atom "H" in standard residue "GLY".
> 
> I have a Gly in position 1, does this depends on the NH protonation?
> 
> Also, I fixed most of the residues, including Gly 1, trying to minimize a small region (Fixed Atoms: selected, in minimize panel) but still have the same errors.
> 
> How can I solve it?
> 
> Thanks for your help,
> 
> Best
> 
> Marco
> 
> 
> -- 
> Dr Marco Sette, PhD.
> Department of Chemical Sciences and Technology
> University of Rome, "Tor Vergata"
> via della Ricerca Scientifica, 00133, Rome, Italy
> e-mail: sette at uniroma2.it
> Tel.: +39-0672594424
> 
> 
> -- 
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