[Chimera-users] No MMTK name for atom "HD2" in standard residue ASN

Sina Analoui sanaloui at bu.edu
Wed Mar 31 12:48:43 PDT 2021

Thank you so much!!! This worked perfectly. In the future, should I just
use the report bug feature for any questions I have about the software such
as this one?

On Wed, Mar 31, 2021 at 1:53 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Usually with similar errors we need people to use menu Help... Report a
> Bug and attach the data (instead of sending e-mail here).  However, I think
> you described it enough for this be answered.
> Before that answer, I would advise thinking about whether you really need
> to minimize the structure.  If you haven't mutated/altered the structure
> obtained from the PDB, often minimization won't change it in any meaninful
> way.
> Now to the answer... Options are to (A) delete the glycosylations so that
> ASN will get its normal hydrogens, OR (B) change all the glycosylated ASN
> residues to a different residue name so they will be recognized as
> nonstandard instead of asparagine.
> For (A) If the glycosylation residues are only NAG you can just use command
> delete :NAG
> (Sometimes there are also other glycosylation residues.)  Or you can
> select them from the menu (Select... Residues... NAG) and then delete with
> menu (Actions... Atoms/bonds... delete).
> For (B) To change the glycosylated ASN residues to a different residue
> name, one trick is first add hydrogens and then change the names of only
> the ASN residues with that abnormal hydrogen name, for example something
> like command:
> setattr r type ASG :ASN at HD2
> The new name (ASG in this example) isn't that important as long as you
> choose something that's not a standard amino acid residue name.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Mar 31, 2021, at 9:19 AM, Sina Analoui <sanaloui at bu.edu> wrote:
> >
> > Hi All,
> >
> > I am currently attempting to minimize a large molecule (ACE2 alongside
> the RBM of a spike protein). I Dock Prep both chains (A chain is ACE2) and
> then go on to attempt to minimize them. However, I keep returning this
> error "No MMTK name for atom "HD2" in standard residue ASN"  I have
> attempted to remedy this by rewriting parts of the PDB file and importing
> it back in and have had no success. Is there any way to either remove NAG
> that is associated with these residues or change this hydrogen to something
> feasible? This seems to be an issue for only the ASNs on the A chain and
> not elsewhere on the molecule
> >
> > Thank you in advance for your help
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