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Questions tagged [software]

For questions pertaining to software used by chemists for professional or academic purposes.

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10 votes
5 answers
2k views

How can I calculate the charge distribution of a water molecule?

I would like to obtain the 3D charge density of a water molecule for plotting purposes (i.e. not necessarily super-accurate). I know this is a tough problem, but I'd like to give it a try. Since I'm ...
0 votes
2 answers
946 views

How to get the coordinates of β12 borophene and χ3 borophene?

Can someone tell me how to draw the β12 borophen and χ3 borophene in Materials Studio or any other software? I've just started my project work, and I'm a beginner in this field. I have searched for ...
1 vote
0 answers
62 views

Any Open-Source, Free Software That Can Be Used to Computationally Calculate Binding Affinity Between Two Molecules? [closed]

There are programs out there which calculate the binding affinity between a ligand and a target protein (Autodock 4, Autodock Vina, Chimera... etc). Is there any analogous program that can be used to ...
6 votes
1 answer
6k views

Software to Draw Laboratory Apparatus

So I am preparing a blog post about chemistry for lay people and I have decided to start talking about the basics. It turns out that it would be super useful to create chemical apparatus on demand to ...
10 votes
2 answers
5k views

Extract all structures of Gaussian 09 molecular dynamics calculation using babel?

Is there a way to easily extract all the structures and energies from an ADMP calculation done in Gaussian 09? GaussView can plot them but not export them in a useful way and babel just gives me the ...
6 votes
1 answer
1k views

How to write an entire trajectory into a single PDB file?

I have a trajectory (few frames) that I want to stack together and build a single PDB. I thought either to use VMD or MDAnalysis library. With VMD if I do ...
6 votes
4 answers
2k views

Thermodynamic properties software

I am looking for a software (can be freeware or purchased) to look up water and steam thermodynamic properties (e.g. density, enthalpy, entropy) preferably a macro in excel. What do you use for this ...
-2 votes
1 answer
4k views

Gaussian syntax error on the input line

I ran a Gold complex in Gaussian 09 with the following exact Route Section PBE0/LANL2DZ Opt Freq NoSymm and it gave me this error message: ...
0 votes
0 answers
295 views

Software for drawing biomolecules (with functional groups abbreviated)

I'm sorry if this is OT, but I find myself slowly going insane trying to draw common biomolecules such as Acetyl Coenzym A. The thing is, I just want to draw the acetyl part and then link that to a ...
2 votes
1 answer
3k views

Titration curve equation/function

How can I create a graph of a titration curve (acid-base, strong or weak, not something specific), with an equation or a function. In other words, what is the equation that describes such a curve that ...
10 votes
1 answer
4k views

converting SMILES (or .mol2) to SMARTS

The conversion between different chemical structure formats, e.g. from .mol2 to .xyz, by openbabel may tied to conditions to be met. One example of such a filter is to allow such a conversion only ...
1 vote
1 answer
71 views

How do I expand a selection in Jmol to include entire residues?

I know how to select by distance in Jmol: select within(5, ATP) This selects atoms that are within 5 Angstroms of ATP residues. How do I expand the selection to include the entire residues of the ...
4 votes
1 answer
226 views

Computational determination of the diagram of molecular orbitals of a polyatomic chemical species

A diagram of molecular orbitals for $\ce{H2O}$ would be as follows: The above diagram has been constructed qualitatively following the steps that I have been instructed in various classes on this ...
3 votes
1 answer
283 views

Quantum chemistry Python package to solve the Coupled-Perturbed Hartree–Fock equations

Two of the most well-known Python quantum chemistry pakcages, PySCF and Psi4, can solve the Hartree–Fock equations. However, I am interested in finding analytic derivatives of the electron integrals: $...
0 votes
1 answer
310 views

How to Build Hydrogen Atoms in MOE using SVL

I'm working on automating a process in MOE using SVL commands. I've got pretty much everything worked out, except I can't seem to find anything for building hydrogen atoms using an SVL command (...
2 votes
1 answer
987 views

Converting a CIF file to a .com or .gjf file

I would like to perform DFT calculations and extract atom coordinates for calculations in Gaussian. I am using Mercury and have been able to isolate the atoms that I am interested in simulating. ...
1 vote
0 answers
43 views

How can I save an EEM file on a Fluoromax4?

I'm trying to run excitation-emission matrices on some water samples, but I'm running into some software issues that the manuals aren't helpful for. In order to use R studio to extract my data, I need ...
3 votes
4 answers
305 views

Finding CML files for small molecules

I'm trying to generate a figure for a physics textbook to show examples of the vector addition of dipole moments in small molecules. For this purpose, I would like to render pictures of a bunch of ...
14 votes
1 answer
2k views

Definition of the B3LYP functional in common QC programs

I wanted to use custom functionals with Gaussian and came up with some interesting definitions of the B3LYP functional within Gaussian, Orca and Turbomole, ... $$\small\begin{array}{lcccccc} \hline ...
1 vote
0 answers
31 views

small negative frequencies in DF T optimizations with organic molecules containing CF3 groups [duplicate]

When optimizing by DFT medium-sized organic molecules containing aromatic CF3 groups (for example, adducts involving takemoto's catalyst), the frequency calculation on optimized structures have always ...
6 votes
1 answer
1k views

How to find the largest cyclic substructure with RDKit?

I have a bunch of structures and of each I would like to find the largest cyclic substructure. I'm not a chemist, so I don't know if there is a common terminology for this. I hope, I made it clear ...
1 vote
0 answers
44 views

Is there a computer program capable of showing protein conformational changes based on pH?

As it is known, changes in pH change the attractions between the groups in the side chains of the protein. Acidification can, for example, cause protonation of the $\ce{COO-}$ end to $\ce{COOH},$ ...
7 votes
1 answer
1k views

ORCA: How to plot an adiabatic potential in dihydrogen H2 molecule?

I stared to study ORCA, and I try to obtain classical results for dihydrogen as for example. I need to get a starting point to understand what needs to be done. So, How to plot an adiabatic potential ...
7 votes
1 answer
10k views

ChemDraw: how to change the default aromatic ring style for drawing from SMILES

I'm a beginner at ChemDraw. I'd like to draw a molecule from SMILES and the ring bond should be drawn like the left image: In my case, my image is drawn like the right image. Is there any method to ...
0 votes
1 answer
2k views

How to draw "box"/square arrows in Chemdraw Prime 16.0?

I want to draw arrows like the one in the figure shown (with reagent a beside it) in ChemDraw 16.0 What is the best way to go about this? I couldn't find anything like it in the arrow options in ...
2 votes
1 answer
459 views

How to convert Excel comments to ChemDraw .cdx?

Not sure whether this might be a Superuser or StackOverflow question... but I hope some Chemist can help me with this. I have an Excel table with cells which contain comments "by Cambridge Soft&...
5 votes
3 answers
993 views

What software was used to create these organic reaction scheme figures?

I am aware that software such as ChemDraw, ChemDoodle or MarvinSketch can be used to draw skeletal formulas and the like. But what can I use to draw (in a similarly professional way) reaction schemes, ...
1 vote
0 answers
51 views

Suggestions of GHS-compliant labelling software

Having amassed a rather large collection of reagents and products from previous years of chemistry experiments, I find rather annoying that their labels aren't even close to being standardized to the ...
2 votes
1 answer
263 views

How to create .CIF file from DRX data in a paper, for compound not found in crystallographic database

I tried to recover a .CIF file with the crystal structure for the compound discussed in this 2006 paper, strontium hydroxide octahydrate - $\ce{Sr(OH)2·8H2O}$ - from Cambridge Crystallographic Data ...
11 votes
3 answers
11k views

Program that simulates basic reactions in organic chemistry

To explain - a friend and I have been working on a program that would allow you to draw organic molecules, indicate the conditions, and predict the products. This would be primarily aimed at basic, ...
3 votes
0 answers
20 views

Correlating specific heat (Cp) of a substance with other substance on the basis of similar physio-chemical properties

I am modelling $\ce{H2O2}$ decomposition in ANSYS Chemkin-Pro and I have difficulty finding $C_p$ (specific heat at constant pressure) for liquid $\ce{H2O2}$ for various temperature ranges. My ...
5 votes
1 answer
261 views

Extracting "Crystal Radii" from a CIF file

I'm currently downloading .cif files from various online databases and using openbabel to convert the fractional coordinates that are in the .cif files into .xyz files. The typical output will look ...
5 votes
2 answers
6k views

ChemDraw: Automatic Caption with Number for Molecules

When working on some reaction schemes in ChemDraw, I sometimes forget to add text/captions with numbering and align it with my molecules before placing all the molecules in a reaction scheme and ...
51 votes
1 answer
1k views

How can I update a map/mesh and coordinates in a PyMol session file?

I have a PyMol session file I was using to create my figures. It contains a protein and ligand broken into several groups of atoms with a fair bit of overlap. There are also a few meshes built from ...
2 votes
0 answers
40 views

CP2K Spherical Cell

I'm trying to run a gas phase cluster calculation in CP2K. I want to create an outside force to constrain water molecules that are in the simulation within a radius of a central ion. I want to create ...
7 votes
1 answer
329 views

Using RDKit to determine "nonring, nonterminal atoms"

I am a non-chemist using RDKit to determine the number of "nonring, nonterminal atoms" in a molecule. I can't find anything in the RDKit documentation that helps with "nonterminal"....
8 votes
1 answer
752 views

Using RDKit to count "RR, the number of rigid single or fused ring systems in the molecule"

I am a computer scientist, not a chemist, working with RDKit. I need to compute something described to me as "RR, the number of rigid single or fused ring systems in the molecule." I know I ...
-1 votes
1 answer
253 views

Install MOLDEN in MACOS Big Surf [closed]

I'm trying to install Molden in a MACOS Bigsurf. The steps that I followed: Install the compilers, gfortran,libraries, etc. extract the source from molden page. open the molden5.8 directory and from ...
4 votes
1 answer
241 views

Gaussian16 Raman calculation from IR checkpoint file

I already did an IR frequency calculation for my molecule. Is there any possibility to just run a Raman frequency calculation with the chk file from my IR ...
6 votes
2 answers
20k views

Free software to draw Newman projections

I need to draw Newman projection of a molecule. Particularly 1,2-dicloroethane rotamers, but have no idea if there is any program to do that kind of things. Do you know about some program available ...
0 votes
1 answer
2k views

Software for determining symmetry elements and point group of drawn molecules

The title represents my overall question. I would like to have a software that able to draw molecules (especially coordination complexes) and determine the symmetry elements and point group of the ...
2 votes
0 answers
786 views

How do you optimize an organo-metalic compound containing cerium in in Gaussian?

I am trying to perform optimisation of the molecule attached. I need to get partial charges and frequencies. The issue is that it doesn't converge with following input: ...
0 votes
1 answer
112 views

XSteam IF97 tables (MS Excel version) lack of inputs [closed]

I am using XSteam IF97 to evaluate steam power plant cycles. However, I miss some important input options such as pressure as a function of entropy and temperature ("p_st()") - when I assume ...
5 votes
2 answers
1k views

How to draw protonated benzene (horseshoe) carbocation structure with ChemDraw?

Is there a way to draw the aromatic "horseshoe" (forgot the official name) structure of a protonated benzene cation (arenium) with ChemDraw, and not the cation with double bonds?
1 vote
0 answers
114 views

Inputting liquid species in chemkin pro

I have been trying to model various species decomposition/combustion in Chemkin Pro. Chemkin only lets you to allow to input gas phase and surface site solid species in your input files, but I have ...
14 votes
3 answers
3k views

How can I draw alpha helices in ChemDraw?

I am trying to draw a polyisocyanopeptide with different kinds of monomeric units that intramolecularly interact with one another. However, I wanted to show these connections with its carbon backbone ...
6 votes
1 answer
249 views

In the absence of a physical model, how can I use free software to visualize stereochemistry?

In a different question, the task was to turn a wedge-and-dash representation into a Fischer projection. This involved rotation of a fairly complex molecule - either as a physical model or a mental ...
6 votes
1 answer
228 views

Are there any molecular modeling programs that can build materials made up of three or more elements into a cylindrical shape?

I would like to build a material similar to what is in the image below. I have tried programs such as Material Studio, Quantum ATK, and VNL, but most of them can only do materials with 2 elements.
5 votes
1 answer
9k views

Which software to use to output molecular orbital diagrams? [closed]

I want to output a molecular orbital diagram. Can anyone recommend a software to do this? Also I searched for a python module, but didn't found a pure solution. Maybe I am using the wrong keywords. I ...
5 votes
0 answers
222 views

How do I display a potential energy surface with molden?

I calculated a gaussian scan job for propylcyclohexane with two dihedral angles. Now I want to display a potential energy surface for that molecule with molden. I am new to molden and only found the ...

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