17 votes
Accepted

What are the parameters that need to be calculated to design the structure of a molecule?

Ah, yes, the fun of force-field building. For the answer to a simple geometry optimization, see I. Camps response below. Skip to the end if you want what is a more general answer to building an entire ...
B. Kelly's user avatar
  • 4,366
10 votes

How may I install the latest version of a software?

Development versions of software When version 1.98 was mentioned in the answer that is linked in your question, it said: "Yes, this is in the latest development version (1.98) as I discussed on ...
I have no free time anymore's user avatar
10 votes

Avogadro for Linux -- Input Generators and Submitting Job to QM software?

I am the person who package Avogadro2 as Flatpak. Stumble upon this thread randomly. I was not aware about this issue when I just randomly clicking on things. Not Avogadro power user, just software ...
Andythe_great's user avatar
10 votes
Accepted

Why the Open Babel submenu is faded out in Avogadro 2 and I can't optimize geometry in Mint 20?

Solution: Install Open Babel The underlying cause is that Open Babel was not installed by default as a dependency of Avogadro 2. I think this is odd, as basic features like geometry optimization ...
ksousa's user avatar
  • 4,108
10 votes

What are the parameters that need to be calculated to design the structure of a molecule?

All Gaussian jobs when completed without any error, will have, at the end of the output file, a phrase/thought/quote from someone famous. It is kind off an easteregg. My latest Gaussian successful job ...
Camps's user avatar
  • 23.3k
9 votes
Accepted

How to make the input generator plugin work in Avogadro 2 on GNU/Linux?

tldr; they need to be in certain directories to be found. I don't know why the input generators were not part of the install package. Certainly on Mac, and AFAIK on Windows, they are and should be. On ...
Geoff Hutchison's user avatar
8 votes
Accepted

Chimera or other software to perform protonation states of a protein

H++ H++ is a web service that permits to protonate your macromolecules using using different pH conditions. From its site: H++ is an automated system that computes pK values of ionizable groups in ...
Camps's user avatar
  • 23.3k
7 votes
Accepted

Converting SDF to PDBQT using OpenBabel

Please, check the version of OpenBabel you are using. At least, version 3.1.0 has the pdbqt format implemented: ...
Camps's user avatar
  • 23.3k
7 votes

How to delete a selection with Avogadro2 (Ubuntu 20.x)?

Yes, I saw your post on the forum - not sure why that commit didn't make it in, but I have a pull-request now. The long and short is that while the main "guts" of Avogadro 2 are finished, ...
Geoff Hutchison's user avatar
7 votes
Accepted

How do I cite development version of a software?

Doing what the authors prefer Sometimes the authors will have strong preferences for how they want their work to be cited, so I would often try to ask the authors how they would like me to cite an &...
I have no free time anymore's user avatar
6 votes
Accepted

Is there a way to automate generation of figures from Avogadro?

Yes, this is in the latest development version (1.98) as I discussed on the Avogadro forum. I shared an example script for exporting screenshots for a folder of ...
Geoff Hutchison's user avatar
6 votes

MOPAC: Is there a simple way to display geometry trajectories

I created a Python script to manipulate the MOPAC output, saving a XYZ file with all the structures from the optimization step. Then, the XYZ can be loaded into Jmol software and do the animation. The ...
Camps's user avatar
  • 23.3k
6 votes

Why the Open Babel submenu is faded out in Avogadro 2 and I can't optimize geometry in Mint 20?

Geoff Hutchison might be able to provide a more up to date and authoritative answer, but I can at least point to some explanation of why OpenBabel isn't included by default with Avogadro 2: https://...
Tyberius's user avatar
  • 15.5k
6 votes

How to delete a selection with Avogadro2 (Ubuntu 20.x)?

In the meantime I have found a couple of solutions and I am listing them here for other users, as frankly not many packages allow to easily (via mouse) select atoms and delete them. you can use ...
gluuke's user avatar
  • 493
6 votes
Accepted

Extracting the coordinates of a super cell in Vesta or Avogadro

One option is to use the Atomic Simulation Environment's sort function. The function ase.build.sort() takes a required Atoms ...
Andrew Rosen's user avatar
  • 7,361
6 votes

How to import a .cif file into Avogadro 2?

tldr; Try one of the [nightly builds](https://nightly.link/OpenChemistry/avogadrolibs/workflows/build_cmake/master) Avogadro uses Open Babel to read CIF files, and unfortunately, OB versions before v3 ...
Geoff Hutchison's user avatar
5 votes

How to generate a input file for gaussian in Avogadro 2?

You can use OpenBabel directly to obtain the Gaussian input from command line. OpenBabel supports two types of Gaussian input generation: Gaussian 98/03 Cartesian Input Gaussian Z-matrix Input To ...
Camps's user avatar
  • 23.3k
5 votes

How to make the input generator plugin work in Avogadro 2 on GNU/Linux?

I solved the problem via a simple change in a directory name: When I installed Avogadro2 (1.93.0-3) in Linux Mint 20.1 Xfce (based on Ubuntu 20.04), it installed the auxiliary files (including the ...
Hypersphere's user avatar
5 votes
Accepted

How to make Pd(111) supercell (√3×√3)R30 via VESTA

This would be a pain to do in GUIs like VESTA and Avogadro. In ASE, this can be done just in one line by ase.build.fcc111_root: ...
Shaun Han's user avatar
  • 1,845
4 votes
Accepted

Tool to saturate the dangling bonds at the surface of nanostructures

Atomic simulation environment can do this with the following line of logic. Calculate the number of nearest neighbors for all atoms Select the undercoordinated atoms Calculate the direction away from ...
Tristan Maxson's user avatar
4 votes

Can a tool “Set space group” be useful?

Determining space group symmetry is really useful when going between a CIF (which typically only includes the symmetry-unique atoms) and a calculation (which typically includes all atoms in the unit ...
Geoff Hutchison's user avatar
4 votes
Accepted

Converting molecular structure from Avogadro into LAMMPS coordinate file

My suggestion, frankly, is to use a newer version of Avogadro. The betas of Avogadro2 include a much more substantial LAMMPS input generator. This includes generating both the input and the ...
Geoff Hutchison's user avatar
4 votes

How do I cite development version of a software?

GitHub has added support for CITATION files. Unfortunately, GitHub's support isn't great. It suggests the following BibTeX: ...
Geoff Hutchison's user avatar
4 votes

How to make the input generator plugin work in Avogadro 2 on GNU/Linux?

I found in the Avogadro forum the solution to this problem. Compile the source code by following the simple instructions reported here: https://discuss.avogadro.cc/t/possible-issue-with-debian-ubuntu-...
NickZ's user avatar
  • 1,479
4 votes

How to make the input generator plugin work in Avogadro 2 on GNU/Linux?

Workaround: Install the Windows port of old Avogadro under Linux, using Wine (tested under Mint 20). Not a proper fix, but should get you going while this issue is sorted out by the developers and ...
ksousa's user avatar
  • 4,108
3 votes

Extracting the coordinates of a super cell in Vesta or Avogadro

This is in Avogadro 1.2.0. I will check behavior on Avogadro 2 later: File -> Open -> Choose your cif file Build -> Super Cell Builder -> Choose the number of repeats File -> Save As -&...
WaterMolecule's user avatar
3 votes

How do I cite development version of a software?

First, follow what the publisher says. Failing that, follow your house style. Failing that ask for - if you have to, demand - a style meeting in your house.
Robbie Goodwin's user avatar
3 votes
Accepted

How to pre-optimize metal-organic complexes in RDKit using UFF?

Okay, there's a bunch to answer here, but I'll do my best. Take a look at the page for Tetraamminecopper(2+) sulfate on pubchem. The SMILES on there is incorrect and no geometry can be generated on ...
Geoff Hutchison's user avatar
2 votes
Accepted

How to address 'saveGraphic: Method not found' error in automating the generation of figures in avogadro using Python?

As mentioned in my answer, this is only available in the development version, which will be released as 1.98 soon. So if you're running 1.97 release, the method is not available. In principal, you can ...
Geoff Hutchison's user avatar
2 votes

Converting SDF to PDBQT using OpenBabel

Go here, no need to install, use on the web http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html
Khairul's user avatar
  • 21

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