JDoe
November 13, 2023, 1:04pm
1
I’m looking at my ORCA outfiles right now and it seems like avogadro thinks that Zinc is supposed to be Calcium for some reason. Not just that, but another input file shows Iodine as Nitrogen.
The bond orders are also wrong. I made a comparison between Avogadro 1.20 and 1.98 to verify that it is in fact an issue with 1.98. I’m guessing 1.98 is still rough around the edges for ORCA 5.0.4 files?
Comparison:
Avogadro version: 1.98
https://1drv.ms/f/c/3cd1ce876c7ff5e4/EqPRscQbCAFElWIA6F1G3qcBdKfgteKVA6oWmrz7WS2teg?e=yGUYak
The Orca code is definitely new, but swapping elements is truly weird.
As far as bond orders, it’s also somewhat newer code, but it’s also going to be confused by the initial bonding (e.g, if you have a bond to a “Zinc” that top carbon already has 4 single bonds, so it won’t create a double bond to the nitrogen, etc.)
Okay, that was an easy fix - thanks for the heads-up. (But a bit confused when the “Br” files contained Cl, not bromine!)
OpenChemistry:master ← ghutchis:fix-orca-elements
opened 03:29PM - 13 Nov 23 UTC
Thanks to the forum
https://discuss.avogadro.cc/t/avogadro-1-98-reads-zinc-as-c… alcium/4978
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JDoe
November 13, 2023, 4:15pm
4
yeah I have a lot of these files and I uploaded only two. looks like I fat-fingered the log files and grabbed the wrong one.
No worries… I think we’ve all done similar things - just chuckled when I opened the file and saw chlorines… had to check the file itself.
system
November 16, 2023, 4:38pm
6
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