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

[Elaine Meng]

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