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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 ...
G M's user avatar
  • 9,079
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 ...
pentavalentcarbon's user avatar
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 ...
pentavalentcarbon's user avatar
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 ...
jjgoings's user avatar
  • 2,130
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 ...
user55119's user avatar
  • 16.8k
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....
Wildcat's user avatar
  • 19.1k
13 votes
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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 ...
pentavalentcarbon's user avatar
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 ...
CuriousTree's user avatar
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 ...
hBy2Py's user avatar
  • 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 ...
Martin - マーチン's user avatar
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 ...
andselisk's user avatar
  • 38k
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 ...
S R Maiti's user avatar
  • 5,685
11 votes
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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 ...
Buttonwood's user avatar
  • 30.1k
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 ...
porphyrin's user avatar
  • 30.6k
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 ...
gannex's user avatar
  • 2,344
10 votes

How to run a B2PLYP-D3 calculation in Gaussian 09?

Search for B2PLYP on the Moller-Plesset page: B2PLYPD3 requests the same but with Grimme's D3BJ dispersion [Grimme11, Goerigk11]. The correct D3 parameters will be set for you automatically. <...
pentavalentcarbon's user avatar
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. ...
pentavalentcarbon's user avatar
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-...
andselisk's user avatar
  • 38k
9 votes
Accepted

What is the purpose of Gaussian, itself?

There are several interrelated reasons (disclaimer: I am a GAMESS developer). Gaussian has a lot of features and interoperability. To take your PM3 example. Yes, the results of a PM3 calculation are ...
Jan Jensen's user avatar
  • 4,819
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) ...
Martin - マーチン's user avatar
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 ...
Wildcat's user avatar
  • 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-...
Miro's user avatar
  • 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 ...
Geoff Hutchison's user avatar
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 ...
pentavalentcarbon's user avatar
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; ...
Martin - マーチン's user avatar
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. ...
Buttonwood's user avatar
  • 30.1k
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 ...
levineds's user avatar
  • 3,080
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 ...
Buttonwood's user avatar
  • 30.1k
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 ...
Karsten's user avatar
  • 40.7k

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