Hello guys, the current version of Avogadro in the step to Generate the Orca Input Parameters, changed the format Z-matrix compact from * int 0 1 to * gzmt 0 1, hence the Python scripts dont works. Someone with a Solution? And Thank you Anna ! Awesome Work !
Howdy, enjoying your videos, they make a great intro to Orca and Avogadro and all of the other bits of software you're showing. Great stuff, not many share their secret sauce! But, if it's not too much trouble, there's a couple of minor bits of info which I'd like to know. - When you set up the molecules in Avogadro, after minimisation, all double bonds were in place but then one of the diene's and the dienophile's double bonds appeared to be broken in the next section when you added the Borons. Did you set them up this way in Avogadro then minimised them or is that just how Avogadro rendered them? Also what minimisation method did you use (MM in Avogadro?)? - Can you give us some timing info for your Orca job (B3LYP would be heavy for 4 laptop cores, I'd imagine...)? - Any particular reason you used int coordinates rather than xyz for the Orca input file? Cheers!
Hi Corey, 1) The rendering in Avogadro is purely based on bond lengths, it doesn't understand what resonance is for instance. So you cannot look at a structure and get the bond orders only from visual inspection 2) For organic molecules I like to use MMFF94, for the rest you're stuck with UFF 3) I run my ORCA jobs on a cluster, so I have no idea of the time frames. However, for molecules of this size, if you don't run frequency calculations, you can expect something around an hour on a laptop. Freq is longer 4) I used internal coordinates because the setup was easier(especially for the ghost atoms)
![[ORCA tutorial] H₂O geometry optimization in under 10 mins (2021) [ENG SUB]](http://i.ytimg.com/vi/onU2vPIGunE/mqdefault.jpg)
Hello, Anna, I'm happy to see that you're using ORCA. G09 is good, but today we have (free) more friendly options (like ORCA).
Thanks for your videos.
+Henrique Junior totally agreed!
Hi, I am new in this ORCA world. May I know-is orca free for calculation and, the data are usable for publication??
Thank you Anna for all your Orca tutorials.
Thank you, this tutorial is the GOLD for me
Hello guys, the current version of Avogadro in the step to Generate the Orca Input Parameters, changed the format Z-matrix compact from * int 0 1 to * gzmt 0 1, hence the Python scripts dont works. Someone with a Solution?
And Thank you Anna ! Awesome Work !
many thanks once again @IaNiusha
Hello, what would be the methodology for relaxed PES with only one compound (optimization)?
Howdy, enjoying your videos, they make a great intro to Orca and Avogadro and all of the other bits of software you're showing. Great stuff, not many share their secret sauce! But, if it's not too much trouble, there's a couple of minor bits of info which I'd like to know.
- When you set up the molecules in Avogadro, after minimisation, all double bonds were in place but then one of the diene's and the dienophile's double bonds appeared to be broken in the next section when you added the Borons. Did you set them up this way in Avogadro then minimised them or is that just how Avogadro rendered them? Also what minimisation method did you use (MM in Avogadro?)?
- Can you give us some timing info for your Orca job (B3LYP would be heavy for 4 laptop cores, I'd imagine...)?
- Any particular reason you used int coordinates rather than xyz for the Orca input file?
Cheers!
Hi Corey,
1) The rendering in Avogadro is purely based on bond lengths, it doesn't understand what resonance is for instance. So you cannot look at a structure and get the bond orders only from visual inspection
2) For organic molecules I like to use MMFF94, for the rest you're stuck with UFF
3) I run my ORCA jobs on a cluster, so I have no idea of the time frames. However, for molecules of this size, if you don't run frequency calculations, you can expect something around an hour on a laptop. Freq is longer
4) I used internal coordinates because the setup was easier(especially for the ghost atoms)
What is the logic behind adding constraints? How do I know what my constraints are? Please help.
Hi Anna, The added lines before generating the .inp file (Tutorial 2) for printing do not work in Orca 4.1.1 (9261 .cpp error). Any ideas?
Hello, How can I convert true Z matrix format for ORCA? I don't now how to use python.
you could use Avogadro
Yes. I use avogadro for constructing molecules. Avogadro was downloaded from ORCA web.
Is it possible to create a nonotube in avogadro not using the tool Nanotube Builder?
Hello. I would like to know how I can restart the PES scan. We have a 72 hour calculation limit on our cluster and the job didn't have time to finish.
You can take the last optimized step and restart from there after adjusting the distances or angles that you are scanning to the new values.
Hi, thanks for nice tutorial. How to do dihedral PES Scan by ORCA?
How u generated plot..plz tell in detail
Should you show a reaction more easy?? ahahahahh