Preparing/Visualizing Mopac input/output files using Avogadro and JMol

[@kathahirpara4707]

It helped a lot! Thank you, Sir!!

[@molecularmodelingtutorial2618]

I am glad you liked!

[@kathahirpara4707]

Molecular Modeling Tutorial Sir, I am using Windows 10, and facing problem while running mol1.out file.

[@molecularmodelingtutorial2618]

if you can explain better your problem perhaps I could help

[@kathahirpara4707]

Molecular Modeling Tutorial I got the solution Sir! Thank you!

[@sreejithomkaram]

Good work sir, expecting more it really helps us a lot...

[@molecularmodelingtutorial2618]

Thanks! Didnt have time to make new ones (just in case, check the channel), sorry.

[@abdelkharrat8520]

Do you know how to access the plugins? I'm trying to use the MOPAC plugin and downloaded it from the download plugins option >avogenerators. However I don't seem to see it as an option under the extensions menu and can't seem to access it. Thank you.

[@omarlouazani8220]

Hi thank you for this video it was very useful, i have some difficulty to locating and optimize the transition state if you have some techniques that can you recommend me i will very thankful

[@molecularmodelingtutorial2618]

Thank you Omar. I never determined transition states (TS) with MOPAC and would recommend you to determine it using DFT instead (e.g., Gaussian program), which is much more precise. Determination of TS is not trivial and the best thing to do besides reading a book (e.g., Quantum Chemistry, Ira Levine) is trying to find a good tutorial on KZbin. Regards Rodrigo

[@omarlouazani8220]

​@@molecularmodelingtutorial2618 thank you very much

[@prakritisaraf7572]

Thank you for making the video. I have one query after generating your file is automatically open but I couldn't open that file tell me how to run after this.

[@molecularmodelingtutorial2618]

Thank you. Sorry, didn't understand your question. Which file do you want to open? You can open files via the terminal (command "vi", more complicated) or with any text editor of your operational system (e.g. textpad, textedit, etc).

[@rackshnadevie2871]

Sir, I don't get an intensity plot while visualizing the vibration in avagadro Kindly help me sir

[@molecularmodelingtutorial2618]

Hi Rackshna. It is difficult to say what the problem is...Perhaps try using Gabedit to see if you can visualize the vibration spectrum. Advogadro has some versions which are a bit "buggy" ;-)

[@gildaavendano9474]

hello thanks so much for you helps, but I have question Why does the system say that mopac is not recognized as an internal or external command?

[@molecularmodelingtutorial2618]

Tranks. The command is only recognized if you have already created an „alias“ inside e.g. your ~/.bashrc configuration file and then close and open again the Terminal. Regards