room topic changed to Python based Matter Modeling software: Phonopy, PySmiles, PySCF, etc.: phonopy.github.io/phonopy, pypi.org/project/pysmiles, github.com/pyscf/pyscf, etc. [phonopy] [pycotem] [pyiron] [pymatgen] [pyscf] [python]

Perhaps this step requires a supplementary module. (It is my first contact with PySmiles.)

@NikeDattani It was you adding the link from matter.se to here, correct?

@Buttonwood Yea! Just in case other people in the room don't know the context of your last comment!

If I just add a @nirshahr /just here/ the invited will not see it. Is this .true.? Does it need an explict note + link as comment below the original question / answer on matter.se?

Totally different question: Do you know about an step-by-step example how to compute pKa with MOPAC?

So far, I did not see MOPAC /as such/ with a tag here on matter.se.

Is the estimation of pKa within the scope of matter.se, and MOPAC /at all/ a suitable tool for this?

What I read (so far) that there is a PM6 level of computation, then allowing both to account for water (as solvent, via the dielectric constant explicitly entered)

and a special keyword pKa to to obtain this value for the most «acidic proton».

However, I thought there could / should be a way to compute this /via/ enthalpies and Hess' law, too.

References found /seem/ to prefer Gaussian.

E.g. doi 10.1007/s00214-006-0232-z

and possibly the numbers differ not only from method to method, but from program to program, too.

@Buttonwood You're right that he won't see it if you just type @nirshahr here, because the user needs to already have been in the room in the last 14 days for the ping to work. I guess this is to avoid the case where someone might be annoyed by a ping from absolutely any user, even though they haven't been in the room for the last 5 years!

About MOPAC, unfortunately I don't have experience with it. Perhaps it would be an excellent question for the main site though!

«I will sleep about it» to clear my mind this.

We do need more questions/day :)

Nirshahr just ping one of us with the @ character when you arrive!

«Rome wasn't built in a day», but for now there is need for a rest. roger and out.

Great quote!

@Tyberius sorry for the flags, however it appears that once a user flags, they cannot undo it.

So that's why I made the second flag, to explain what happened. I had no idea this situation would be resolved so quickly at the time of making the first flag!

@Buttonwood in the example, take a look at atom index 3. In pysmiles, it says there is an hydrogen, but rdkit seems to say there isn't (neither an implicit or explicit, since the value you wrote is the total number of hydrogens). Any idea for the difference there?