Questions tagged [avogadro]
For questions about the software AVOGADRO.
25
questions
4
votes
1
answer
68
views
How to make Pd(111) supercell (√3×√3)R30 via VESTA
How to make Pd(111) super-cell (√3×√3)R30 via VESTA or Avogadro software?
- 105
4
votes
1
answer
146
views
Can a tool “Set space group” be useful?
In my program Chemcraft, a popular tool is the “Set point group” utility: it symmetrizes the molecule according to a specified point group, and then the symmetry of the molecule is correctly ...
- 406
3
votes
1
answer
116
views
How to pre-optimize metal-organic complexes in RDKit using UFF?
I have run into a particular problem while trying to automate my input file generation for ORCA calculations. Apparently, I either do not fully understand how SMILES strings work, or I am demanding ...
- 443
3
votes
1
answer
235
views
Converting molecular structure from Avogadro into LAMMPS coordinate file
I am new to LAMMPS and have been working my way through available examples before diving into my own research using LAAMPS. I am currently working through the tutorial given here: https://avogadro.cc/...
- 63
8
votes
3
answers
1k
views
How do I cite development version of a software?
Does anyone know how to cite the developmental version of Avogadro 2 version 1.98 mentioned here or unpublished software in general?
I have found a BibTeX citation here though this is for a generic ...
- 123
8
votes
1
answer
391
views
How may I install the latest version of a software?
This is a follow-up of my previous question here: How to address 'saveGraphic: Method not found' error in automating the generation of figures in avogadro using Python?, at which I was told to ...
- 151
6
votes
1
answer
90
views
How to address 'saveGraphic: Method not found' error in automating the generation of figures in avogadro using Python?
My question is a follow-up question to this question posted by Hemanth Haridas.
I ran the example .py script in Geoff Hutchison's answer for the above mentioned question to generate .png files from ....
- 151
7
votes
1
answer
100
views
Is there a way to automate generation of figures from Avogadro?
I have a collection of molecules represented by SMILES codes, along with their corresponding 3D coordinates. I want to efficiently generate figures for these structures using Avogadro. Ideally, I ...
- 2,792
3
votes
0
answers
200
views
How can we build a polymer from a monomer in Avogadro? [closed]
I have been trying to reproduce a geometry optimization from a research paper, where it was done by Avogadro.
However, I cannot find the option for building a polymer from a monomer. I am using ...
2
votes
0
answers
96
views
Generating unit cell from an optimized molecule in Avogadro?
I am trying to generate the unit cell for a material from the optimized coordinates of a molecule. I am able to generate an orthorhombic unit cell from the coordinates using utilities in Avogadro. ...
- 2,792
3
votes
0
answers
38
views
Prevent Avogadro from clipping wavefunction plots [closed]
When I try to plot wavefunctions in the Avogadro software I find that the orbitals are often clipped by a rectangular box. Does anyone know how to increase the size of this box so that I can plot ...
pQ12branch
10
votes
0
answers
1k
views
How to visualize natural atomic orbitals from PySCF [closed]
I'm trying to visualize the different methods of getting localized orbital (LO) given in the User Guide. I went through the example, saved the orbitals as cube files, then opened the files in ...
- 303
5
votes
1
answer
150
views
Tool to saturate the dangling bonds at the surface of nanostructures
When it comes to studying 2D, 1D or 0D nanomaterials, saturating the dangling bonds in the surface helps remove unwanted localized surface states from the band structure 1. However, so far I have not ...
- 2,613
8
votes
1
answer
807
views
How to generate a input file for gaussian in Avogadro 2? [duplicate]
I made auto optimization working by installing openbabel using sudo apt install openbabel.
Is there any way to make Gaussian extension working by doing something?
I'...
- 81
2
votes
0
answers
52
views
Chemical Structure of Iron Manganese Silicate Nanoparticle (IMSN) Nanozyme? [closed]
Hope you're doing well. Actually I am working on a project related to DNA regulated Nanozyme and I have a nanozyme of mesoporous silica "Iron Manganese Silicate nanoparticle (IMSN) nanozyme"....
- 81
8
votes
1
answer
398
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, ...
- 367
8
votes
1
answer
210
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 ...
- 131
7
votes
2
answers
4k
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 ...
- 367
10
votes
1
answer
1k
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 ...
user2026
8
votes
2
answers
781
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 ...
user2026
11
votes
2
answers
615
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 ...
- 493
12
votes
5
answers
3k
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....
- 4,048
7
votes
2
answers
3k
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....
- 4,048
11
votes
0
answers
1k
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 ...
- 349
15
votes
2
answers
806
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(...
- 1,407