Questions tagged [software]

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

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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 ...
5
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1answer
76 views

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 ...
5
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1answer
88 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 ...
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34 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 $\ce{COOH},$ ...
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0answers
8 views

Converting SDF to PDBQT using OpenBabel [migrated]

I want to convert several molecules from sdf format to pdbqt using OpenBabel. However, I can't find ...
1
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1answer
67 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 ...
6
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1answer
201 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 ...
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1answer
49 views

How to get the coordinates or .cif file of β𝟏𝟐 𝐛𝐨𝐫𝐨𝐩𝐡𝐞𝐧𝐞 and χ𝟑 𝐛𝐨𝐫𝐨𝐩𝐡𝐞𝐧𝐞?

Can someone tell me how to draw the β𝟏𝟐 𝐛𝐨𝐫𝐨𝐩𝐡𝐞𝐧𝐞 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. ...
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1answer
67 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 ...
6
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1answer
699 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 ...
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0answers
20 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 ...
3
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0answers
49 views

Obtaining electron density from orbital information in the Molden format [closed]

I'm trying to obtain an electron density from orbital information written in the Molden format by the formula, $$ \rho(\mathbf{r}) = \sum_{i}^{occ} |\phi_{i}(\mathbf{r})|^{2}. $$ Is there any post-...
7
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1answer
52 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"....
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1answer
104 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 ...
4
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1answer
61 views

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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1answer
74 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 ...
3
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1answer
61 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 ...
3
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0answers
13 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 ...
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1answer
221 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 ...
0
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1answer
57 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 ...
1
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1answer
145 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
17 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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0answers
30 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 ...
13
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3answers
1k 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
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1answer
175 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
92 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
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1answer
2k 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 ...
4
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2answers
726 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
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0answers
122 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....
6
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1answer
435 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
324 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
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0answers
72 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
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1answer
437 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 ...
2
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1answer
81 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 ...
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0answers
241 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
41 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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0answers
184 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
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1answer
73 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
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0answers
82 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 ...
1
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1answer
207 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
59 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 ...
6
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3answers
367 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
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0answers
40 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
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1answer
150 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.
6
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1answer
93 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
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1answer
573 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
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1answer
101 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
59 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
265 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
190 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 ...

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