Questions tagged [software]
For questions pertaining to software used by chemists for professional or academic purposes.
358
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Does the 3D structure generated with MolView violate the wedge-dash rules of "above/below the plane"?
I've been taught that in a wedge-dash diagram, the wedge represents a bond above the plane of the paper, and the dash represents a bond below the plane.
Accordingly, I expected the structure of this ...
- 273
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Reaction kinetics data for ethylene dimerization to produce but-1-ene
I am trying to simulate ethylene dimerization reactor (CSTR) in which Ethylene (in gas form) will be feed to a liquid phase reactor (operating at 50-53 deg. C temperature and 23 bar (g) via sparger ...
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Creating custom spectra graphs
I wanted to make a few custom spectra graphs for some homework questions I'm assigning. The issue is that the Education Board issued datasheets do not reflect online images. They often say that bonds ...
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Is There a Problem with the Assignment of Stereochemical Descriptors by ChemDraw in Select Examples?
While using ChemDraw Professional 21.0.0.28 to construct some cyclic allenes and rotationally restricted biphenyls, I came across anomalous assignments of stereochemistry. [For the latest version of ...
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How to compute the electronic energy reported by Gaussian from the AlphaOrbitalEnergies?
I followed the instructions on Wolfram Language & System Documentation Center — FCHK (.fchk) to analyze the *.fchk file.
I ran an energy calculation with ...
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Crystal packing prediction for simple organic molecules?
Is it yet possible to predict a simple organic molecule's crystal structure or how the molecules arrange in a crystal without diffraction measurements?
By crystal structure I mean, how would molecules ...
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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 ...
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Troubleshooting an Autodock Vina Error on Chimera: "Could not find an atomic number for Hn Hn"
After having minimized a ligand (that I prepared on Marvinsketch), and after having prepared a target enzyme to dock said ligand onto (collected from RCSP PDB), I was met with an error by the reply ...
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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 ...
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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 ...
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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 ...
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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 ...
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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:
$...
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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 (...
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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. ...
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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 ...
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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 ...
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Discrepancy when calulating mol weights with ChemSketch and Python RDKit
I am an IT guy with little knowledge of Chemistry, so please bear with me...
For context: I am working with a system that has a lot of structures, their .mol files ...
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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 ...
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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 $\ce{COOH},$ ...
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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 ...
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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 ...
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358
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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 ...
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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 ...
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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 ...
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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 ...
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99
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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"....
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265
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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 ...
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Which quantum chemistry approximation to use?
I'm just getting started with quantum chemistry using some simple test problems. I have a few of the software packages installed (ASE, Psi4, GPAW etc) and everything is working - no issues with the ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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&...
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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 ...
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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 ...
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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 ...
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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 ...
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Computational chemistry software to generate files of cartesian coordinates and zmatrix of molecules
Is there any software that I can provide bond lengths, bond angles and torsion dihedrals of a molecule and generate an output file in the format of cartesian coordinates or zmatrix?
Example:
I would ...
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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 ...
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How to convert an XYZ file to Z-matrix?
I would like to generate a Z-matrix from the following XYZ file (C2H6dimer.xyz):
...
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Is there a Python module for calculating Ovality of a molecule?
Ovality gives a measure of how the shape of a molecule approaches a sphere (at one extreme) or a cigar shape (at the other). Ovality is described by a ratio of volume to area (see https://en.wikipedia....
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Alternative python modules to RDKit to convert SMILES to structure
Python module RDKit is great, but it cannot be installed by pip, and therefore it is difficult to use it sometimes in a virtual environment.
I am wondering that if ...
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An automated approach to visualize several xyz structures
I have several .xyz files (each composed of several molecules) and I'd like to find an automated way to visualize and save them. I'd appreciate any guidance.
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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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685
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MolView is unable to generate correct 3D structure for hydroxypropadiene
MolView is unable to generate the correct structure of hydroxypropadiene. It instead generates the structure of acrolein (which has the same molecular formula). Why is this so? Is it because ...
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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 ...
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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:
...
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Chemical simulation software for a person who is not in the chemistry field but has a basic knowledge about chemistry [closed]
In my research I need to see, if I mix chemical A with chemical B, then what is the outcome? if it's another chemical, then I need to see the resultant chemical's 1. Density 2. Melting point 3....
