19
votes
Accepted
Creating energy profile diagrams for publication
PyEnergyDiagrams
I use my own script. I have posted it on GitHub now.
This is the final result:
It is quite easy to use, on the GitHub readme there is a small tutorial. You have to create an ...
- 9,089
16
votes
Accepted
Python package for modelling chemical reactions
This is not really my area of expertise, but a quick search for "python chemical reactions" revealed three hits I've never seen before that may be of interest, the first one being closest to what you ...
- 7,529
16
votes
Accepted
How to calculate Lennard-Jones potential with quantum mechanical methods
Yes, this is technically possible. A basic tutorial for this is in the excellent Psi4Numpy project, which I'll reproduce here with minor modifications. Their example fits the counterpoise-corrected ...
- 7,529
15
votes
Accepted
How to visualise the total electron density from a Gaussian 16 calculation?
When GaussView gives you the error
Surface build failed! Processing mesh, No data to plot. IsoValue may be out of range
it means that the data in your .cube ...
- 2,120
15
votes
How can I draw alpha helices in ChemDraw?
I use ChemDraw Professional 19.1.1.32. If you follow File>Open Templates>Advanced BioDraw, you will find the black helix that I have reoriented from horizontal to vertical. The red helix was ...
- 17.3k
13
votes
Is Orca wrongly breaking bonds? Why can it only optimize the molecule with COPT activated?
It seems to be a bug with optimization in internal coordinates. As I already mentioned in comments, ORCA couldn't converge at geometry relaxation step when optimization is done in internal coordinates....
- 19.1k
13
votes
Accepted
What does the format nF10.8 mean?
It is a Fortran format specifier.
It means
$n$: repeat the input $n$ times, once for each weight
F: input is a floating-point number
10.8: the number is of total width 10 (including the decimal ...
- 7,529
13
votes
How can I draw alpha helices in ChemDraw?
This illustration may be a combination of two images, or simply a program I don't know about. However, there are many (3D) protein visualisation programs that can show alpha-helices such as PyMol, VMD ...
- 918
11
votes
Accepted
How to specify a different isotope in the ORCA quantum chemistry program?
ORCA cannot read isotope information from XYZ files -- the OpenBabel specification does not include it and so ORCA doesn't look for it in the geometry file.
You need to copy-paste the geometry into ...
- 17.4k
11
votes
How do I perform a partial optimisation in GAMESS?
Unfortunately GAMESS is not as user friendly as other quantum chemistry packages, so when it comes to running non-standard calculations a little bit more effort is necessary.
First of all I recommend ...
- 44.3k
11
votes
Accepted
ChemDraw: how to change the default aromatic ring style for drawing from SMILES
From pp. 91–92 ChemDraw 20.0 User Guide, PDF version shipped with the ChemOffice suite:
Toggle Aromatic Display
An aromatic structure can be displayed either as an alternating double and single bond ...
- 38.4k
11
votes
Accepted
ORCA: How to plot an adiabatic potential in dihydrogen H2 molecule?
By adiabatic, I presume you mean the Born-Oppenheimer approximation (which is usually used). If you need a plot of potential against H-H distance, then you need to do a relaxed potential energy ...
- 5,725
11
votes
Accepted
Discrepancy when calulating mol weights with ChemSketch and Python RDKit
In first place, you must clarify with the users of the database the purpose of the entries about molecular weight because average molecular weight and exact molecular weight differ in their meaning ...
- 30.6k
11
votes
Accepted
Software to draw one-dimensional PES including vibrational energy levels
I have made this basic python 3 script which runs in a Jupyter notebook (or in Visual Studio Code). With different molecules you will need to adjust the plot scale. The first 10 levels are plotted ...
- 31k
10
votes
How to find a transition state for an electrophilic addition with Gaussian and map the reaction pathway?
I would like to build on LordStryker's well-written guide by providing some elementary examples of input file formatting for these calculations.
Now that I've re-read the question, I see that my ...
- 2,354
10
votes
Gaussian Error: Zero Point Energy Calculation on Fluoroform fails
As you can see in the error message
#T B3LYP/6â€311+G(3df,2p)
there is some Unicode garbage in your input file; the dash between the 6 and 3 isn't an ASCII dash. ...
- 7,529
10
votes
Accepted
What software was used to create these organic reaction scheme figures?
$\mathrm\LaTeX$ to the rescue
I reproduced these reaction schemes with $\mathrm\LaTeX$ using the following particular packages:
chemfig for drawing 2D chemical structures (note that I enabled sans-...
- 38.4k
9
votes
How should elements be colored? And how many bonds does an atom have?
To extend on Philipp's excellent answer, I'd like to offer some advice on judging bond orders. Pekka Pyykkö and Michiko Atsumi published covalent (single-, double-, triple-) bond radii for (almost) ...
- 44.3k
9
votes
Accepted
Does SCF energy mean same as HF energy?
Answering your question from the title: no, SCF does not necessarily mean HF. Essentially the same self-consistent field (SCF) procedure is used to solve both the Hartree-Fock (HF) equations and the ...
- 19.1k
9
votes
Accepted
Modeling 3-center-2-electron bonds in Avogadro
First of all, I am not an Avogadro developer, just an occasional user. My view of this matter is the following:
As 3D molecular drawing/editing software, Avogradro, does not need to "understand" B-H-...
- 146
9
votes
Modeling 3-center-2-electron bonds in Avogadro
I'm the developer of Avogadro.
Beyond the other answer, which is excellent, I want to emphasize two things:
There is no rigorous definition of a "bond" in computational chemistry, particularly ...
- 28k
9
votes
Accepted
Extract all structures of Gaussian 09 molecular dynamics calculation using babel?
If you have the latest copy of cclib installed, it can extract both the energies and geometries and write the geometries to an XYZ trajectory file that you can open with Avogadro or VMD.
To print the ...
- 7,529
9
votes
Accepted
How to obtain the radial probability distribution function from a quantum chemical calculation?
This is gladly not a big problem as MultiWFN (open source) can do that for you. I'll guide you through the process from start to finish. My current setup is Gaussian 09 Rev D.01 and MultiWFN 3.3.8; ...
- 44.3k
9
votes
Easiest way (software) to visualize charge density from an .xyz file with point-charges?
After the successful calulation of the electrostatic surface potential, molden equally allows the display of it in a form like
(source)
A step-by-step, hopefully still functional, tutorial is this. ...
- 30.6k
9
votes
Accepted
Molecular orbitals used with CCSD(T) geometries
Pulling together some of my comments into an answer:
The principal question at issue is "what do you mean by orbitals?", which is partially related to "what do you want to look at them for?" You can ...
- 3,070
9
votes
Accepted
Software for generating a lattice from a unit cell for molecular crystals?
In addition to the presentations about CCDC Mercury and Vesta by @andselisk here and later mine about Avogadro could be extended. As described earlier, Avogadro's capability to read .cif files about ...
- 30.6k
9
votes
Software recommendations for overlaying molecular structures
The compare command in free and open source programs Jmol (offline) or JSmol (online) outputs the root mean square of the pairwise differences (RMSD) as well as the ...
- 41.5k
9
votes
Accepted
Alternative python modules to RDKit to convert SMILES to structure
I am not aware of any other Python tool not mentioned in the question @Mithoron linked to. Openbabel is available via pip by the way.
That RDKit is not available on PyPi should not hinder you from ...
- 264
9
votes
Which software to use to output molecular orbital diagrams?
If your interest is a qualitative reprepresentation, you may reach out for an editor like inkscape and use lines, squares and Unicode to create a picture like the following one
In text fields you may ...
- 30.6k
Only top scored, non community-wiki answers of a minimum length are eligible