Very grateful for this video. I had been struggling for some time to be able to generate and display molecular orbitals for a class I teach, but my knowledge of quantum mechanics is a bit limited due to have completed studies long ago. So, this was a breakthrough! Fortunately, the older version of Avogadro on my laptop can handle the out file, though the newer version on my desktop can't! It is the laptop I use in class. However, I needed to install the 64 bit ORCA on the desktop since the laptop has 32 bit debian. In any case it is not a big deal to generate the out file on the desktop, transfer it to the laptop and use its Avogadro version for the teaching.
Thank you for this easy-to-understand tutorial! I was looking for a good lightweight orbital visualizer, and it was just that ~5 lines of code in the .inp file that made the difference. Subscribed!
Thank you for the video. I just want to add a piece of important info. If anyone wants to add the auxiliary basis sets in ORCA 4 (and later versions), use def2/J, def2/JK, etc... instead of def2-SYP/J, def2-SYP/JK that was generated by Avogrado. Or else you would get an error of duplicate command.
Thanks for your tutorials, Dear laNiusha, How I can find the spin multiplicity for transition metal complexes while creating an input file for ORCA? Please guide me?
Thanks a Ton!!!! Was stuck in Population Analysis for more then a week. :) Keep Them Coming. Please Include GROMACS and AUTODOCK too... Tutorials which are available are too complex for beginners. #VoiceOfAnAngel :)
Hi! First of all, thank you so much for making these tutorials; they really are wonderful. I had a question about displayed orbitals from geometry optimizations. Are the HOMO/LUMO values for those orbitals which are displayed in Avogadro accurate after just a geometry optimization? Or is there another step to correctly calculate these values? Thank you so much!
Sorry, I didn't get a notification fro your comment. Avogadro is only a display tool. It takes what ORCA has calculated, and makes it visual. If your ORCA calculation ran well, then your orbitals will be fine.
First of all, thank you very much for making these videos. Secondly, I would like to ask a question, why can't I read the output file with Avogadro software and cause an error: Reading molecular file failed.
Muchas gracias! de verdad desde hace tiempo estaba buscando hacer esto. ¿Cómo podría calcularse el mapa de potencial electrostático utilizando orca? Saludos desde colombia, de verdad muchas gracias!
Hi laNiusha! Thank you for your nice tutorial! That`s really help me a lot! But I have a problem that after I run the optimization, the orbital energy values and statues I got were different with yours. what is wrong with that? Thank you again for your kind help!
thank u mam its very nice. can you do it for the inclusion complexes of cyclodextrin . i did it but it says line no ..... missing and command stops. if any body can help please help, i will be higly thankful to him whoever will help.
I have done optimization and NBO calculation by using ORCA but the output file is not opening in avogadro. How can I visualize the HOMO LUMO ? Thank you so much in advance.
Hello! Thank you for the wonderful video! I want to ask how to make a negatively charged atom in the ORCA input file. I write" Z -1" after xyz specification. But program not running.
Not exactly. I need to charge a particular atom, leaving the overall system charge neutral. Well, or indicate a specific electron number for a given atom. The task is as follows: there is a coordination center (+2) and two ligands (-1). The total charge of the system as a whole is neutral. How to enter this in the input file?
That is, to calculate the organometallic complex, I just enter its structure without introducing a specification for the metal? The program itself will teach the population of electronic levels of the coordination center?
Hi, I am very much a beginner to this. When I try to run orca, my input file cannot be opened. The file is not read only, and I ma pretty sure I have the path right. What else could it be?
Hi, I make these videos on my spare time, and now that I got a full time job, there is very little time left for me to work on tutorials :( but there are lots of good resources on the WWW that can help you out! Good luck
+IaNiusha Im new to computational chemistry and am learning ORCA+Avogadro (Thanks for the Tutorials btw ) but i wanted to run some NBO/NPA without having to pay $100 for NBO6.0 so i found this open source software JANPA that does the same. But i cant figure out how to use it with avogadro (it says its meant for molden)...is there a way???
Hi! I'm new in ORCA. And also in Avogadro. My problem is that at the GUI of Avogadro, clicking the 'Extensions', I can't find the Orca option. I'm using ORCA and AVOGADRO under linux. Do you know a way to integrate the two? Thank you!
Hey Warlock, I think that the guys at Avogadro haven't added the ORCA extension in the Linus version of Avogadro. You could use Gabeit even though I don't particularly like it myself.
Hi! Sorry! Have watched your "Avogadro with ORCA Tutorial: system setup" video and have seen that no linux support yet. Thanks for replying though. I'm now trying to use the windows versions. Great job on the tutorials. They are very helpful. Please keep it up! :)
Thanks Dear, Yeah I get output file without error and can be open on Avogadro, but I am not sure, why these two files (as mentioned above) are missing? there must be some error, But I could not find it. please guide me If you have some idea about it..Thanks for your time
Hi when you generated the file, did you leave the calculation section as single point energy? I did that at first, and was missing the same two files. Before I realized my mistake and changed the calculation to Geometry optimization.
+dannic234that means you have installed a version of Avogadro that does not support ORCA. please refer to the video of how to setup ORCA for full explanation : th-cam.com/video/NTk62asaz8Y/w-d-xo.html
![[ORCA tutorial] H₂O geometry optimization in under 10 mins (2021) [ENG SUB]](/img/n.gif)
Very grateful for this video. I had been struggling for some time to be able to generate and display molecular orbitals for a class I teach, but my knowledge of quantum mechanics is a bit limited due to have completed studies long ago. So, this was a breakthrough! Fortunately, the older version of Avogadro on my laptop can handle the out file, though the newer version on my desktop can't! It is the laptop I use in class. However, I needed to install the 64 bit ORCA on the desktop since the laptop has 32 bit debian. In any case it is not a big deal to generate the out file on the desktop, transfer it to the laptop and use its Avogadro version for the teaching.
Thank you for this easy-to-understand tutorial! I was looking for a good lightweight orbital visualizer, and it was just that ~5 lines of code in the .inp file that made the difference.
Subscribed!
Thank you for the video. I just want to add a piece of important info. If anyone wants to add the auxiliary basis sets in ORCA 4 (and later versions), use def2/J, def2/JK, etc... instead of def2-SYP/J, def2-SYP/JK that was generated by Avogrado. Or else you would get an error of duplicate command.
reference sites.google.com/site/orcainputlibrary/basis-sets
love it so much, thank you you help me so nice!
Thanks for your tutorials, Dear laNiusha, How I can find the spin multiplicity for transition metal complexes while creating an input file for ORCA? Please guide me?
Thanks a Ton!!!! Was stuck in Population Analysis for more then a week. :) Keep Them Coming. Please Include GROMACS and AUTODOCK too... Tutorials which are available are too complex for beginners. #VoiceOfAnAngel :)
Hi! First of all, thank you so much for making these tutorials; they really are wonderful. I had a question about displayed orbitals from geometry optimizations. Are the HOMO/LUMO values for those orbitals which are displayed in Avogadro accurate after just a geometry optimization? Or is there another step to correctly calculate these values? Thank you so much!
Sorry, I didn't get a notification fro your comment. Avogadro is only a display tool. It takes what ORCA has calculated, and makes it visual. If your ORCA calculation ran well, then your orbitals will be fine.
molto buono.
Gracie
(You have sweet voice!)
First of all, thank you very much for making these videos. Secondly, I would like to ask a question, why can't I read the output file with Avogadro software and cause an error: Reading molecular file failed.
then there must be an error in your output file somewhere....
Muchas gracias! de verdad desde hace tiempo estaba buscando hacer esto. ¿Cómo podría calcularse el mapa de potencial electrostático utilizando orca? Saludos desde colombia, de verdad muchas gracias!
Ma'am I have calculated G_solv energy by using orca. Can I calculate G_gas by using this software? If possible please reply.
WHY DONT I GET THE "HURRAY" MESSAGE? But it does says that "ORCA TERMINATED NORMALLY" Pls tell me how to get that "Hurray" status..thanks!😊
love this! :D
Hi laNiusha! Thank you for your nice tutorial! That`s really help me a lot! But I have a problem that after I run the optimization, the orbital energy values and statues I got were different with yours. what is wrong with that? Thank you again for your kind help!
and actually I did not find the "HURRAR" in the output file
@@yidahuang4493 hurray
hello madam. the output MO's of c6h6 molecule comes at the center of avogadro screen. how can i solve the problem ??
How to copy 4 code lines in 2:40 ? Where can I find that?
thank u mam its very nice.
can you do it for the inclusion complexes of cyclodextrin .
i did it but it says line no ..... missing and command stops.
if any body can help please help, i will be higly thankful to him whoever will help.
Can we convert output files into pdb?
I have done optimization and NBO calculation by using ORCA but the output file is not opening in avogadro. How can I visualize the HOMO LUMO ? Thank you so much in advance.
Hello! Thank you for the wonderful video!
I want to ask how to make a negatively charged atom in the ORCA input file.
I write" Z -1" after xyz specification. But program not running.
Or should the number of electrons be indicated as a charge?
For example, for Ni2+, it will be Z 26
* xyz charge multiplicity
ex: *xyz 2 1 or *xyz -1 3
Not exactly.
I need to charge a particular atom, leaving the overall system charge neutral. Well, or indicate a specific electron number for a given atom. The task is as follows: there is a coordination center (+2) and two ligands (-1). The total charge of the system as a whole is neutral. How to enter this in the input file?
you dont. you give the overall charge always. the program assigns the charges based on the wavefunction computed
That is, to calculate the organometallic complex, I just enter its structure without introducing a specification for the metal? The program itself will teach the population of electronic levels of the coordination center?
Hi, I am very much a beginner to this. When I try to run orca, my input file cannot be opened. The file is not read only, and I ma pretty sure I have the path right. What else could it be?
Can you please offer complete course in ORCA ? Particularly on HF and DFT
Hi, I make these videos on my spare time, and now that I got a full time job, there is very little time left for me to work on tutorials :( but there are lots of good resources on the WWW that can help you out! Good luck
@@IaNiushaIaNiusha please mention the website name which is missing ...please
Hi. I cannot get the avogadro.out file. Why is that? Please help. Thank you.
very nice!!
+IaNiusha Im new to computational chemistry and am learning ORCA+Avogadro (Thanks for the Tutorials btw ) but i wanted to run some NBO/NPA without having to pay $100 for NBO6.0 so i found this open source software JANPA that does the same. But i cant figure out how to use it with avogadro (it says its meant for molden)...is there a way???
yes, working on it!
hi, my avogadro haven't extension to orca.... i want used to orca_plot program to molecule orbitals. How open molecule orbital to used avogadro.?
You could use it, but it won't come out nicely. Use Gabeit or VMD then.
you have to install the Avogadro version from the ORCA forum, that will have the needed support for ORCA
Hi! I'm new in ORCA. And also in Avogadro. My problem is that at the GUI of Avogadro, clicking the 'Extensions', I can't find the Orca option. I'm using ORCA and AVOGADRO under linux. Do you know a way to integrate the two? Thank you!
Hey Warlock, I think that the guys at Avogadro haven't added the ORCA extension in the Linus version of Avogadro. You could use Gabeit even though I don't particularly like it myself.
Hi! Sorry! Have watched your "Avogadro with ORCA Tutorial: system setup" video and have seen that no linux support yet. Thanks for replying though. I'm now trying to use the windows versions. Great job on the tutorials. They are very helpful. Please keep it up! :)
thank you!
no, that means that your calculation haven't converged to a stable geometry and died before it ended. Run it for longer and make sure it ends properly
try downloading from here: avogadro.cc/news/avogadro-1-2-0-released/
Thanks
Love your accent. Are you Argentinian?
Thanks for Tutorial, But I have problem after running ORCA I have just 4 files instead of 6 files, .xyz and .trj files showed missing? please reply
are you sure your job completed without errors?
Thanks Dear, Yeah I get output file without error and can be open on Avogadro, but I am not sure, why these two files (as mentioned above) are missing? there must be some error, But I could not find it. please guide me If you have some idea about it..Thanks for your time
you can use my script called OUT_2_XYZ.py from here (github.com/Ianiusha/Uselfuls_Scripts) to extract the tranjectory file from your output file
thanks dear for your cooperation and sincerity, yeah it worked
Hi when you generated the file, did you leave the calculation section as single point energy? I did that at first, and was missing the same two files. Before I realized my mistake and changed the calculation to Geometry optimization.
My version of Avogadro does not have the option for orca in the 'extensions' tab. Have I not set it up correctly or is there something I am missing?
+dannic234that means you have installed a version of Avogadro that does not support ORCA. please refer to the video of how to setup ORCA for full explanation : th-cam.com/video/NTk62asaz8Y/w-d-xo.html
try downloading from here: avogadro.cc/news/avogadro-1-2-0-released/
thanks once again...
thanks