Questions tagged [avogadro]

For questions about the software AVOGADRO.

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8
votes
1answer
109 views

Chimera or other software to perform protonation states of a protein

I want to perform a Molecular Docking between some ligands and a protein in different pH conditions. For this, I calculated the distance between atoms in different pH concentrations for the ligands, ...
8
votes
1answer
123 views

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

Regarding input generators for a Linux (Linux Mint 20.1 Xfce) version of Avogadro2, I have managed to get this working using the Flatpak version and copying the input generator python scripts from ...
7
votes
2answers
98 views

Converting SDF to PDBQT using OpenBabel

I want to convert several molecules from sdf format to pdbqt using OpenBabel. However, I can't find ...
10
votes
1answer
141 views

How to import a .cif file into Avogadro 2?

I downloaded the latest version of Avogadro2 (1.91.0), but it appears I can't open a .cif file in this software. Is there a way around this? In an earlier version of Avogadro, I remember being able to ...
8
votes
2answers
190 views

Extracting the coordinates of a super cell in Vesta or Avogadro

I am trying to use a program such as Vesta or Avogadro to build a super cell from a .cif file for a molecular crystal. In neither program can I seem to figure out how to order the output of the ...
11
votes
2answers
222 views

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

For reason that I did not understand Avogadro has been phased out of Ubuntu 20.x and the available package Avogadro2 is instead another branch of the package, which ...
11
votes
4answers
768 views

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

It seems Avogadro was phased out in Ubuntu 20.04 (Focal Fossa) and derivatives like Mint 20 (Ulyana). Now the version available in the repositories is Avogadro 2. If you had Avogadro installed in 18....
7
votes
2answers
955 views

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

It seems Avogadro was phased out in Ubuntu 20.04 (Focal Fossa) and derivatives like Mint 20 (Ulyana). Now the version available in the repositories is Avogadro 2. If you had Avogadro installed in 18....
11
votes
0answers
292 views

How to convert a molecular structure made in Avogadro to a LAMMPS coordinate file? [closed]

I was trying to convert a crystal structure into a LAMMPS data file in Avogadro but whenever I type .lmpdat as an extension, it says "The file name is not valid". Can you tell me any ...
14
votes
2answers
255 views

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

Before performing Molecular Dynamics on a co-polymer that doesn't have a ready-to-use structure anywhere, the monomer fragment was built in Avogadro software with 0 net charge, B3LYP theory and 6-31G(...