[Chimera-users] Problem with minimizing structure

Eric Pettersen pett at cgl.ucsf.edu
Thu Jul 26 11:13:20 PDT 2018

Hi Renee,
	For standard residues, Chimera simply looks up the Amber atom type and partial charge (both needed for minimization) in a table based on the atom’s name.  Obviously for this to work the atom needs to have the appropriate PDB-standard name.  There is no ‘H1’ atom in standard PDB GLN residues.
	Typically the easiest way to remedy this, since you are about to minimize the structure anyway, is to delete the existing hydrogens and let Chimera add them back during the minimization prep — which will ensure they have the correct names in most cases.  The one case I can think of where that doesn’t work is if there are backbone heavy atoms missing in a residue.  In that situation it may be best to delete the residue entirely.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Jul 25, 2018, at 4:03 PM, Renee Arias <rarias72 at gmail.com> wrote:
> Hello all,
> I am having a problem with the minimizing structure function in Chimera. I am just trying to change a single residue on a very small protein (88 residues), but I keep getting the error: No MMTK name for atom "H1" in standard residue "GLN". Previous message boards seem to just point to bug fixes in Chimera, but I am running the newest version available for Windows 10. 
> I would appreciate any help!
> Thanks so much,
> Renee
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