Questions tagged [software]
For questions pertaining to software used by chemists for professional or academic purposes.
353
questions
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33 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 ...
-3
votes
0answers
27 views
Autodock Vina Error on Chimera: Service "local" unavailable [migrated]
I was confronted with an error, upon trying to dock a minimized ligand to a target protein, that the "service 'local' [is] unavailable". I then realized that one must have an executable file ...
1
vote
0answers
31 views
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 ...
6
votes
1answer
101 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 ...
0
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0answers
35 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 ...
4
votes
1answer
61 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 ...
1
vote
1answer
39 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 ...
3
votes
1answer
103 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
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1answer
62 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
1answer
209 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
0answers
34 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 ...
1
vote
0answers
23 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
1answer
117 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
votes
1answer
234 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
0answers
37 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 $\ce{COOH},$ ...
2
votes
1answer
214 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
votes
1answer
305 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 ...
0
votes
2answers
209 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
votes
1answer
241 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
votes
1answer
2k 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 ...
2
votes
0answers
25 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
1answer
70 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
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1answer
186 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
votes
1answer
74 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
147 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
1answer
100 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
votes
0answers
14 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 ...
0
votes
1answer
596 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
votes
1answer
61 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
vote
1answer
258 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
25 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
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0answers
36 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
2k 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
1answer
189 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 ...
1
vote
1answer
189 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
4k 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
votes
2answers
1k 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
154 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....
7
votes
1answer
660 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 ...
3
votes
2answers
557 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
93 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
580 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
votes
1answer
106 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 ...
1
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0answers
377 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
45 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
311 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
87 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
102 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
vote
1answer
309 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
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0answers
66 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 ...
