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 ...
  • 4,086
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 ...
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 ...
  • 19.9k
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 ...
9 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 ...
  • 3,758
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 ...
  • 19.9k
7 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 ...
  • 6,971
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, ...
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: ...
  • 19.9k
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 ...
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 ...
  • 493
5 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://...
  • 14.4k
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 ...
  • 19.9k
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 ...
4 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 ...
3 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-...
  • 1,429
3 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 ...
  • 3,758
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 -&...
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
  • 21

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