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

[Elaine Meng]

No, not for any question: Report a Bug is for when you get an error message or think there might be some bug in the program, and/or when you need to attach your specific data to show the problem.

For other questions, we first encourage you to look at the Chimera User Guide
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/index.html>

...(or search it with menu: Help... Search Documentation) 

...and Chimera tutorials: 
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>
<https://www.rbvi.ucsf.edu/chimera/tutorials.html>

However, if you still can't figure out how to do something, or want to find out if something is possible, you can ask here on chimera-users at cgl.ucsf.edu

Best,
Elaine

> On Mar 31, 2021, at 12:48 PM, Sina Analoui <sanaloui at bu.edu> wrote:
> 
> 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