[Chimera-users] Problem with minimizing structure

[Renee Arias]

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
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription:
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180726/d2d0c40d/attachment.html>