[Chimera-users] Problem with minimizing structure

Elaine Meng meng at cgl.ucsf.edu
Thu Jul 26 13:38:57 PDT 2018

Hi Renee,
Only the following monatomic ions are handled:
 "Li+, Na+, K+, Rb+, Cs+, F–, Cl–, Br–, I–, Mg2+, Ca2+, Zn2+. In addition, Fe ion nonbonded parameters are taken from the heme residue in the Amber parameter database."

You could try text-editing your input PDB file to change copper to whichever of the choices above is most similar.

Although it’s theoretically possible to add parameters for more ions (see the bottom of the page linked above), it’s difficult even if you know what values the ion should have, and not generally recommended.
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 26, 2018, at 11:58 AM, Renee Arias <rarias72 at gmail.com> wrote:
> Hi Eric,
> I gave your advice a try with the following steps:
> First, I just deleted residue 88, which was giving me problems in the first place.
> Fetch 2VB2
> del H
> Then added them back with Tools, Structure Editing, AddH
> Minimize structure, kept default steps, etc
> Memorize options chosen in subsequent dialogs
> Unchecked "Add hydrogens" 
> And I got a structure that looked like this, which obviously not correct. The original structure starts with the copper out in the middle, coordinated by the Mets and the His. For some reason it moves the copper over to the histidine, and then distorts the histidine in a strange way. Do you know what I could be doing wrong here?
> <image.png>
> Thanks a lot for your help,
> Renee
> On Thu, Jul 26, 2018 at 11:16 AM Renee Arias <rarias72 at gmail.com> wrote:
> Thanks so much! I will give it a try!
> On Thu, Jul 26, 2018 at 11:14 AM Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 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> 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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