Questions tagged [software]

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

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57 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&...
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0answers
13 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 ...
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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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3answers
760 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 ...
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1answer
167 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 ...
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1answer
55 views

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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1answer
406 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 ...
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2answers
152 views

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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0answers
86 views

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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1answer
234 views

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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1answer
68 views

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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57 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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1answer
212 views

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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104 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: ...
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1answer
38 views

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....
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87 views

How to fix 'error: hangup' in Gaussian 16 modredundant scan calcuation?

I have got a problem during my calculations with Gaussian 16. Everytime I start a job to scan the energy about 2 dihydrals I run into the following Error: hangup. I ...
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1answer
57 views

I'd like to model some compounds with DFTB, but some elements don't have parameter files in the official site. Is there a workaround?

I was reading a bit about this technique, Density Functional based Tight binding (DFTB). It's claimed it can provide a speed improvement of several fold when compared to plain DFT, still giving ...
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48 views

What are the alternatives we have to the VEDA 4 vibrational energy distribution analysis software?

Said software is very useful when you need to assign the peaks in vibrational spectra to different vibrational modes found in a hessian calculation for a given molecule, as described in Jamróz, Michał ...
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1answer
102 views

Determine and draw planes and axes of symmetry of a molecule using software (VESTA or Mercury)

I designed the $\text{MoS}_2$ molecule (bilayer), with polytype 2H in the VESTA. My goal is to draw the plans and axes of symmetry of the bilayer set. According to the information in the literature, ...
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0answers
44 views

How to model the Belousov-Zhabotinsky (BZ) (in Maple) [closed]

I need to model the Belousov-Zhabotinsky reaction (or a different oscillating one). I found out about the Oregonator and the Brusselator reaction and now I want to model them in Maple (or similar ...
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2answers
255 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, ...
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36 views

How does one calculate the electronic difference density in practice?

I am interested in calculating electronic difference density maps. These have been described for quite a long time by Bader and others. For example, below is the fourth of a series of papers which ...
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1answer
131 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.
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1answer
78 views

Are there any semiempirical methods that work with heavy alkaline earth metals?

I did some research. Found some semiempirical methods that work even with heavy lanthanide compounds (RM1). But could not find any references to semiempirical methods compatible with the heavier ...
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1answer
252 views

How to reproduce the Gaussian 09 SDD basis set in Gamess-US?

I'm trying to migrate away from Gaussian 09, using Gamess-US instead for molecular modelling of some heavy alkaline earth metal complexes, using density functional theory (DFT). In some of my previous ...
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1answer
58 views

Software for simulating NMR spectra [duplicate]

I am wondering is there any open source software that predict NMR spectra by giving the chemical shift? Something like Spinach library http://spindynamics.org/group/?page_id=12 (Matlab is not free, ...
3
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1answer
50 views

How to access implicit bond angles that don't appear in Gaussian's z-matrix input?

Suppose I have a Gaussian script to calculate the energy of a relatively large molecule like hexamethyldisiloxane: ...
7
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1answer
178 views

How to obtain curve energy and non-bonded interaction parameters (e.g. Lennard Jones parameters) with Gaussian?

I am parameterizing a force field and would need to obtain non-bonded interaction parameters of atoms (e.g., Lennard-Jones parameters). My primary idea is to obtain a potential energy curve using the ...
3
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1answer
127 views

How to perform Mulliken population analysis by hand with GAMESS output?

I did a simple calculation on hydrogen fluoride with GAMESS and I wanted to reproduce the Mulliken population analysis for atomic orbitals. A molecular orbital is a linear combination of atomic ...
3
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1answer
100 views

How to obtain the radial probability distribution function of a given orbital from a quantum chemical calculation?

I know that a very similar question has already been asked here and a very competent and useful answer has been provided (see here). However, that previous question was related to the total electron ...
3
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1answer
30 views

MOPAC: can we run THERMO immediately after the geometry optimzation?

With MOPAC, I am trying to set up single run with geometry optimization followed by calculation of THERMOdynamic parameters. Is there viable way for that?
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1answer
62 views

What are some software packages that allow visualization of molecules in 3D? [closed]

Could anyone suggest a good application or a software that helps visualise molecular structures in 3d? I have tried a few applications like King Draw and molecular constructor but I want to know if ...
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70 views

Reaction energies of solids from quantum chemistry?

I was reading a paper by Catlow et al. [1], and they mentioned the dissolution of copper into copper ions, which is given by this equation: $$\ce{Cu2O(s) + 2 h+ <=> Cu+(aq) + 1/2 O2(g)} \tag{...
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1answer
290 views

How do I convert an Excel file with SMILES and IC50 to .smi file? [closed]

Not much else to say, I have an Excel file with two columns and I need to create a .smi from it.
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1answer
319 views

Software to assist drawing of complex, three-dimensional skeletal formula from scratch or from existing crystal structure

Is there a tool that would help in creating rather intricate line drawings (not pre-rendered balls-and-sticks/wireframe/sticks/ORTEP diagrams) for a skeletal formula in 3D space? To illustrate the ...
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0answers
87 views

Valency of each atom in a molecule with python

Consider ethanol, where each carbon atom has a valency of 4 and oxygen a valency of -2. I would like to determine these values for many compounds given their SMILES or InChI keys. (For the purpose of ...
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2answers
570 views

Software for generating a lattice from a unit cell for molecular crystals?

I am looking for a software package which can take a unit cell (and lattice parameters, etc.) and from that generate a crystal lattice. Ideally it will have functionality for orthorhombic, hexagonal, ...
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1answer
278 views

Using AutoDock Vina to dock multiple ligands to multiple receptors?

I am trying do that what the title depicts, but I keep running into errors creating the executable script. Is it even possible to automate the docking of multiple ligands to multiple receptors? ...
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2answers
128 views

Computing force fields using Open Babel

I am trying to use Open Babel (OB) to compute universal force field (UFF) given an xyz file. I read each xyz file and turn it ...
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0answers
54 views

Sources for files for testing a thermal ellipsoid (ORTEP) program

I am trying to reimplement the functionality of the classical program ORTEP for producing thermal ellipsoid plots of a crystal/molecule in a modern computer language. Unfortunately, I am having ...
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133 views

How to extract force constants for normal modes from ORCA?

I am following the computational method described in Scientific Reports.[1] Where the authors analyze the contribution of each excited state normal-modes to the shift of the transition energy. For ...
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1answer
94 views

Software that determines whether a molecule can exist and draw it from a formula?

I have run calculations that predict atomic configurations. As a simple example, in a system that contains H and O, I might get a list like: ...
5
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2answers
141 views

Freely available software for generating 3D coordinates of molecules

As part of some research I am doing, I want to do a head-to-head comparison of software for generating 3D atomic coordinates for molecules. Is there a list anywhere of chemical software that does this?...
6
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0answers
222 views

OpenBabel: how to get correct SMILES from Gaussian output?

I would like to get the molecular structure as SMILES from Gaussian output files. OpenBabel seems to be the tool made for such tasks. However, the structure is not always correct. One example: ...
4
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1answer
64 views

Red Squares in RDKit?

I'm newish to RDKit and couldn't find an answer to this online. The following is a minimal representation of how I drew a molecule ...
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0answers
340 views

Cloud-based molecular modeling software

I’m an IT Acquisitions and Licensing specialist researching well-supported cloud software alternatives to Fujitsu’s molecular modeling SCiGRESS. I am coming in with a tech background, but little to ...
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1answer
307 views

Why does the SCF not converge in a structure optimization with GAMESS of the thiourea molecule at the PM6 level of theory?

I'm using GAMESS to run a geometry optimization on a thiourea molecule, using PM6. However, the output file keeps displaying the error message, "NO FORCE FIELD, SCF DOES NOT CONVERGE." Is there an ...
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1answer
25 views

How do I calculate the proportion of respective conjugates of one base mixed with several acids (and/or conversely) at different temperatures? [closed]

How do I calculate the proportion of respective conjugates of one base mixed with several acids (and/or conversely) at different temperatures, and is there a free software tool that would allow me to ...
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1answer
40 views

Is there a way to export detailed data about atom connectivity, dihedral angle, etc from GaussView?

As far as I know, opening the .com files as .txt files (with a text editor like simple notepad) yields a nicely formatted table ...

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