-
Notifications
You must be signed in to change notification settings - Fork 279
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
GLH residue code #1855
Comments
Is there a canonical reference for these codes? It's all slightly confusing as a non-biophysicist |
I agree that these naming conventions are confusing and can be different in different communities. I'd probably stay close to the definitions of amino acid residues given in the major force fields. E.g. GLH is defined in the amber force field (e.g. compare this line ). Unfortunately, I don't have a good canonical reference list or dictionary. |
The three letter codes are defined by the PDB. The names used by Amber are nonstandard and conflict with the PDB definitions. |
True. It seems, and maybe @peastman can confirm, that the mdtraj one-letter code definitions are actually taken from the PDB chemical component dictionary. About the current case: The PDB's definition of GLH gives a one-latter code Q, GLN as parent comp id, and name "N-5-CYCLOHEXYL-N-5-[(CYCLOHEXYLAMINO)CARBONYL]GLUTAMINE". So this isn't a different protonation state of a standard amino acid but a more complex chemical modification. In my experience, if you open a random MD simulation, the chances are pretty low that a residue named GLH actually refers to this, and very high that it's a protonated GLU from an amber-based simulation. This means that the output of |
Correct - this allows us to follow a fairly robust standard to any possible force field used and be compatible with experimental structural biology standards. Especially since, as stated above by Peter:
It looks like we do support the protonated form in |
Hi, I think the one-residue-code of GLH is wrong in
mdtraj.core.residue_names._AMINO_ACID_CODES
:mdtraj/mdtraj/core/residue_names.py
Line 107 in 36b4cee
It should be a protonated GLU (E), not a protonated GLN (Q).
The text was updated successfully, but these errors were encountered: