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Questions tagged [avogadro]

For questions about the software AVOGADRO.

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6 votes
1 answer
148 views

MOPAC: Is there a simple way to display geometry trajectories

I would like to display MOPAC geometry trajectories for structure minimization and transition state searching. Is there a simple way to achieve that ? Avogadro can display only final geometry from ...
Miro Iliaš's user avatar
4 votes
1 answer
153 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?
Rubi Agrawal's user avatar
4 votes
1 answer
170 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 ...
Linkey's user avatar
  • 406
4 votes
1 answer
326 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 ...
J.Doe's user avatar
  • 493
4 votes
1 answer
398 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/...
Baba Booey's user avatar
9 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Does anyone know how to cite the developmental version of Avogadro 2 version 1.98 mentioned here or unpublished software in general?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 ...
Xiong Sichao's user avatar
8 votes
1 answer
406 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 ...
Aimun Jawed's user avatar
6 votes
1 answer
94 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 ....
Aimun Jawed's user avatar
7 votes
1 answer
118 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 ...
Hemanth Haridas's user avatar
3 votes
0 answers
288 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 ...
Unni Krishnan's user avatar
2 votes
0 answers
120 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. ...
Hemanth Haridas's user avatar
3 votes
0 answers
41 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 ...
user avatar
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 ...
Steve Cox's user avatar
  • 303
5 votes
1 answer
168 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 ...
PBH's user avatar
  • 2,653
8 votes
1 answer
972 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'...
In_Chem's user avatar
  • 81
2 votes
0 answers
53 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"....
user4100's user avatar
8 votes
1 answer
491 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, ...
RoyBatty's user avatar
  • 367
8 votes
1 answer
221 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 ...
Hypersphere's user avatar
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 ...
RoyBatty's user avatar
  • 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 ...
user avatar
8 votes
2 answers
886 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 ...
user avatar
11 votes
2 answers
686 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 ...
gluuke's user avatar
  • 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....
ksousa's user avatar
  • 4,108
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....
ksousa's user avatar
  • 4,108
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 ...
Abdullah Arafat's user avatar
15 votes
2 answers
874 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(...
Kavya Mrudula's user avatar