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 force-field. Read the whole thing if you want some insight into force-fields, particularly partial charges.
First, doing an electronic structure calculation (...
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 packager.
Anyway, we are looking into that, but will probably take some time, since there is no detail error for us to work with at the moment.
I suspect that ...
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 finished with this quote:
THERE IS NO SCIENCE WITHOUT FANCY, NOR ART WITHOUT FACTS.
-- VLADIMIR NABAKOV
Anyway, answering your second question:
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 the other hand, Linux package maintainers often have rules about how they're supposed to handle such things and perhaps it's a separate package.
In Avogadro 2, ...
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 depend on it. Anyway, just installing Open Babel separately fixed the problem. To install it, open the terminal and input the following command:
sudo apt install ...
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 macromolecules and adds missing hydrogen atoms according to the
specified pH of the environment. Given a (PDB) structure file on
input, H++ outputs the completed ...
One option is to use the Atomic Simulation Environment's sort function. The function ase.build.sort() takes a required Atoms object (e.g. the supercell of the original CIF) and an optional tags argument that allows you to sort however you wish. It's then just up to you to find out how to flag each individual molecule in the order that you'd like.
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, there's a lot of small pieces that need to be done (case in point). Help is always welcome - there are plenty of tasks that can be done in a few hours for anyone ...
Please, check the version of OpenBabel you are using. At least, version 3.1.0 has the pdbqt format implemented:
# obabel -v
No input file or format spec or possibly a misplaced option.
Most options must come after the input files. (-i -o -O -m can be anywhwere.)
Open Babel 3.1.0 -- Jan 11 2021 -- 11:51:22
# obabel -L formats
abinit -- ABINIT Output ...
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 would break molecules such that all atoms fit within the unit cell. Typically, most people would rather have a contiguous molecule even if it goes through a ...
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 chimera as it offers the same feature via CTRL+mouse:
https://www.cgl.ucsf.edu/chimera/data/downloads/1.15/linux_x86_64.html and then menu Actions -> Atoms/Bonds -...
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://blog.kitware.com/avogadro-2-and-open-chemistry/
The important points of the article are:
The developers wanted to separate the Avogadro application from the ...
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 run OpenBabel:
obabel [-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options]
Take a look at this answer for ...
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 input generators) in the following directory:
However, the Avogadro2 application looks in the following ...
I found in the Avogadro forum the solution to this problem. Compile the source code by following the simple instructions reported here:
I tried and it worked for me.
It seems to be a bug with the packaging process.
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 packagers. It's possible to install the standalone .exe version of the old Avogadro for Windows under Linux, using Wine. Wine is a compatibility layer, used by ...
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 -> Choose desired file type (XYZ and PDB work. Avogadro 1.2.0 seems to lock up on my system when I try to write mol2 files by this procedure.
I would guess ...
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 the neighbors (sum vectors from
neighbor->atom and normalize)
Add your atom to cover the dangling bonds, such as H, in direction
of calculated vector