Avogadro 2.1.0: Trp aminoacid is with unbound atoms

Miroslav_Ilias · October 23, 2026, 10:46pm

Dear support,

with the newest Avogadro 2.1.0 I wantedto build some peptide, but the Trp aminoacid is incomplete, with unbound atoms:

ghutchis · October 24, 2026, 12:51am

That’s weird - sorry. I’ll admit we don’t use Trp in any of our experiments, so I didn’t notice. Probably been there for a while - looks like it’s because Trp uses the generic elements instead of the PDB atom names. (Oh, it looks like a bug in the generating script.)

The big fix is in the fragments repository (i.e., the TRP.zmat .. and ARG.zmat too) and there’s a separate minor bug with N+ formal charges building. The continuous release should have it in a few hours.

github.com/OpenChemistry/avogadrolibs

Fix some minor peptide builder bugs (#3230)

master ← ghutchis:fix-peptide-builder-residues

opened 12:47AM - 24 Oct 26 UTC

ghutchis

+123 -0

Prompted by Miroslav Ilias in the forum (Trp bug) - added entries for SEC, PYL, …AIB, and NME - added a formal charge step for N+ (i.e. bond order four for N) Developer Certificate of Origin Version 1.1 Copyright (C) 2004, 2006 The Linux Foundation and its contributors. 1 Letterman Drive Suite D4700 San Francisco, CA, 94129 Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Developer's Certificate of Origin 1.1 By making a contribution to this project, I certify that: (a) The contribution was created in whole or in part by me and I have the right to submit it under the open source license indicated in the file; or (b) The contribution is based upon previous work that, to the best of my knowledge, is covered under an appropriate open source license and I have the right under that license to submit that work with modifications, whether created in whole or in part by me, under the same open source license (unless I am permitted to submit under a different license), as indicated in the file; or (c) The contribution was provided directly to me by some other person who certified (a), (b) or (c) and I have not modified it. (d) I understand and agree that this project and the contribution are public and that a record of the contribution (including all personal information I submit with it, including my sign-off) is maintained indefinitely and may be redistributed consistent with this project or the open source license(s) involved.