No MMTK name for atom "HD2" in standard residue ASN
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
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@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@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
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@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@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@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
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@cgl.ucsf.edu
Best, Elaine
On Mar 31, 2021, at 12:48 PM, Sina Analoui sanaloui@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@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@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@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
participants (2)
-
Elaine Meng -
Sina Analoui