openmolecules.org

 
Home » DataWarrior » Bug Reports » Pentavalent carbonyl issue (urea formation?) (Enumerating combinatorial library)
Pentavalent carbonyl issue (urea formation?) [message #1938] Thu, 22 June 2023 21:14 Go to previous message
padster is currently offline  padster
Messages: 5
Registered: June 2023
Junior Member
Hi, I am trying to create a combinatorial library (macrocyclic peptide) in DataWarrior. The issue I run into however is that every amide bond forms correctly with the next amino acid, but for some reason it also forms a bond (red bond in image) between the N and C=O of the same amino acid, creating a urea-like motif (refer to image attached). If the red bond is deleted, it forms the correct structure. Curiously, this issue does not happen when running DW on Mac. Is there a way to fix this on Windows so that it runs correctly as well, or is there some sort of setting that changes this? I reinstalled DW, but still run into the same issue.

Macrocycle: /forum/index.php?t=getfile&id=727&private=0
Reaction: /forum/index.php?t=getfile&id=728&private=0

Report message to a moderator

[Message index]
 
Read Message
Read Message
Read Message
Read Message
Read Message
Read Message
Read Message
Read Message
Previous Topic: conformer generation sometimes skips isomer generation
Next Topic: conformer generation misses some entries
Goto Forum:
  

[ Syndicate this forum (XML) ] [ RSS ] [ PDF ]

Current Time: Fri Oct 17 22:01:16 CEST 2025

Total time taken to generate the page: 1.02041 seconds
openmolecules.org