[Chimera-users] Problem with minimizing structure

[Eric Pettersen]

Forgot to mention that one easy way to delete all hydrogens is with the command “del H” (Favorites→Command Line).

—Eric

> On Jul 26, 2018, at 11:13 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> 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
> 
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
> 
> 
> 
>> On Jul 25, 2018, at 4:03 PM, Renee Arias <rarias72 at gmail.com <mailto: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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