Questions tagged [software]
For questions pertaining to software used by chemists for professional or academic purposes.
324
questions
0
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1answer
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&...
1
vote
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 ...
1
vote
0answers
15 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 ...
12
votes
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 ...
5
votes
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 ...
0
votes
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 ...
3
votes
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 ...
3
votes
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):
...
3
votes
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....
4
votes
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 ...
1
vote
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.
5
votes
0answers
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 ...
4
votes
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 ...
0
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0answers
49 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 - $\ce{Sr(OH)2Ā·8H2O}$ - from Cambridge Crystallographic Data ...
1
vote
0answers
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:
...
-4
votes
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....
0
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0answers
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 ...
3
votes
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 ...
2
votes
0answers
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 JamrĆ³z, MichaÅ ...
1
vote
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, ...
1
vote
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 ...
4
votes
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, ...
3
votes
0answers
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 ...
6
votes
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.
5
votes
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 ...
2
votes
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 ...
2
votes
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
votes
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
votes
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
votes
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
votes
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
votes
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?
-1
votes
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 ...
0
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0answers
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{...
-2
votes
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.
12
votes
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 ...
1
vote
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 ...
9
votes
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, ...
-1
votes
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?
...
1
vote
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 ...
3
votes
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 ...
6
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0answers
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 ...
0
votes
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
votes
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
votes
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
...
7
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0answers
340 views
Cloud-based molecular modeling software
Iām an IT Acquisitions and Licensing specialist researching well-supported cloud software alternatives to Fujitsuās molecular modeling SCiGRESS. I am coming in with a tech background, but little to ...
5
votes
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 ...
0
votes
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 ...
0
votes
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 ...
