Questions tagged [software]
For questions pertaining to software used by chemists for professional or academic purposes.
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Software or library for creating images of ball and stick models?
Is there any code library (in any programming language) or software capable of producing images of ball and stick diagrams?
Example of an image of a ball and stick model for Ammonia:
(Image source)
...
7
votes
1answer
67 views
converting SMILES (or .mol2) to SMARTS
The conversion between different chemical structure formats, e.g. from .mol2 to .xyz, by openbabel may tied to conditions to be met. One example of such a filter is to allow such a conversion only ...
2
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0answers
28 views
Rotating dihedral and Angles And Generate File For Each Degree
I need to optimize a force field I generated. For this, I should apply Genetic Algorithm (G.A). To apply G.A I should do this for 220 molecules:
1) Find all dihedrals for each molecule ( I did this ...
4
votes
0answers
42 views
Software for computations of rovibrational states' energies and corresponding spectroscopic constants in diatomic molecules
I need to compute rovibrational energy levels and also the spectroscopic constants, especially $\omega_e$ to compare my results with other papers.
So far I've tried LEVEL16, which seems very ...
3
votes
0answers
82 views
DFT Exchange-Correlation Two Electron Integrals
Are there any electronic structure programs that print the exchange-correlation (XC) integrals for a given DFT functional? These integrals are of the form $$\langle pq|w|rs\rangle$$
where $w$ is an XC ...
2
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0answers
31 views
How to obtain spectroscopic constants Omega_e, Alpha_e, B_e, D_e and D_0 from centrifugal constants?
I need to compute a spectroscopic constants of $N_2^+$ states and I would like to do it using LEVEL16 software, due to its high interpolation flexibility.
But it seems, that LEVEL16 can only compute ...
2
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0answers
40 views
ApexTrack: peak tail looks like a shoulder
I'm trying to implement ApexTrack algorithm in my software by following the description written by Waters. But many chromatograms that I see have noticeable tailing of peaks: .
No matter what ...
3
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0answers
25 views
How can I save and read the CI vector during CASSCF calculations in Gaussian?
I have searched through the GAUSSIAN 16 manual and have not been able to solve these two related issues:
(1) I want to be able to save the CI vector and load it as an initial guess for a different ...
3
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0answers
48 views
How to get the second electron affinity of tellurium?
I need the value of the second electron affinity of Te, i.e. the energy change associated with the attachment of an electron to a $\ce{Te-}$ anion
$$\ce{Te- + e- -> Te^{2-}}$$
In the books (e.g. J. ...
2
votes
1answer
48 views
How to prepare a Gaussian input file for a binary solvent?
The UV absorption energy spectrum of a molecule has been recorded experimentally using binary solvent (DMSO:Water=9:1 v/v). I am trying to calculate the absorption energy of the same molecule using ...
4
votes
1answer
89 views
How to draw protonated benzene (horseshoe) carbocation structure with ChemDraw?
Is there a way to draw the aromatic "horseshoe" (forgot the official name) structure of a protonated benzene cation (arenium) with ChemDraw, and not the cation with double bonds?
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1answer
96 views
Gaussian syntax error on the input line
I ran a Gold complex in Gaussian 09 with the following exact Route Section PBE0/LANL2DZ Opt Freq NoSymm and
it gave me this error message:
...
5
votes
1answer
33 views
Help with missing output from cubegen utility after density calculation in Gaussian16
I am busy trying to do density calculations in Gaussian16 as I need the .cube output for input to the PIXEL software. But my Gaussian output seems to be missing an entire chunk of data and I don't ...
11
votes
2answers
120 views
Molecular orbitals used with CCSD(T) geometries
Suppose I am given some geometry data (say, of a water dimer) from CCSD(T). If I were to do a single-point energy calculation to generate orbitals for the system, wouldn't CCSD give something more ...
4
votes
1answer
422 views
Illustrator to chemdraw [closed]
I am not sure that this is the right place for this question, but I'll try.
I am working on a scheme that I am developing on illustrator. I have a lot of chemical structure and plus I have some ...
3
votes
1answer
54 views
Why is the ROHF spin density of the propenyl radical not symmetric?
I was preparing some material for my students and in order to illustrate the concept of spin density and how the ROHF method gives a purer description of this property than the UHF method. I prepared ...
5
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0answers
67 views
Ab initio MD simulations in VASP
I'm not sure if this is an appropriate question for Chemistry.SE, but I'm taking a stab. I'm running ab initio MD calculations in VASP and I'm trying to optimize different input tags. On the VASP ...
7
votes
2answers
109 views
What library/program can draw molecules in 3D programmatically?
Molecular graphics software is usually interactive.
But I am looking for a library or program that would be able to render a given molecule based on the commands from another program. I would like to ...
2
votes
2answers
137 views
How To Scan “improper dihedrals” in Gaussian 09?
I am trying to parameterize Amber force field for a novel molecule, but I couldn't obtain improper dihedrals. Because if I scan impropers like dihedrals; later or sooner the molecule is overlapping ...
2
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0answers
43 views
Generating density matrix of a wavefunction from common quantum chemistry software
I am looking for density matrixes for a couple of closed shell and open-shell systems, and I wonder if there is a trivial way to make e.g. Gaussian just generate an output for me. I may be wrong but ...
2
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0answers
37 views
Geometry optimisation in Gaussian09
I have looked at various sources regarding this, including the Gaussian official website. However, I have not managed to understand the geometry optimisation method used by Gaussian, a method known as ...
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1answer
50 views
Software for the atom model of all elements [closed]
I want an atom model with shells but I haven't found one yet and the only software that created an atom was Cinema 4D. This software is not for beginners like me and I used a tutorial to make an atom ...
5
votes
1answer
132 views
Raman spectra in Gaussian [closed]
I want to simulate Raman spectra of benzene in Gaussian 09.
Calculated spectra for a single ring Benzene ($\ce{C6H6}$) in Gaussian differs about $\pu{40 cm^{-1}}$ for each peak, compared with ...
3
votes
1answer
73 views
Is there a way to check reactions? [closed]
I'm very new to organic chemistry.
I would like to practise simple reactions (HX + Alkenes, X2 with Alkenes and so on) with examples i create myself. Is there a way to check if my products are ...
0
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1answer
55 views
ChemDraw temporary label for chemnum LaTeX
Currently I'm searching for a nice way to implement my ChemDraw graphics into $\mathrm{\LaTeX}$.
There is a package called chemnum which will auto-label the ...
1
vote
1answer
93 views
Molpro - Connection between atomic term symbols and system symmetry
Let's say I have a carbon atom with the electron configuration $1s^22s^22p^2$. We know, that using atomic term symbols we can describe the following states:
$${}^3P_0, {}^3P_1, {}^3P_2, {}^1D_2, {}^...
3
votes
1answer
49 views
Why is the active space for the dinitrogen cation defined this large in my example?
I have a Molpro script which computes $\ce{N2^+}$ potential energies.
The significant part is the input for the wave function:
...
2
votes
1answer
54 views
How do I have to interpret the input to the OCC flag in Molpro?
I'm trying to understand the occupied orbital specification in Molpro. They're specified by the OCC flag, while it's stated in the documentation, that
OCC, m1, m2, ..., mn;
where the ...
3
votes
1answer
116 views
Molpro - Simple explanation of OCC, CORE, FROZEN and CLOSED orbitals
I'm beginning with quantum chemistry and I'm supposed to do some ab initio calculations with Molpro. The problem is, I don't understand the orbital specification very well.
Let's say, I have the ...
-1
votes
1answer
122 views
How to type condensed formulas in ChemDraw?
What I want is shown in the bubble 1, while what I keep getting every time I change the single bond to a double bond is shown in bubble 2. The H of the middle C in bubble 2 keeps shifting down when I ...
2
votes
0answers
90 views
Restarting a Gaussian partially constrained relaxed surface scan using GICs
I am Using Gaussian 16 rev D.01, and I want to perform relaxed surface scans where I vary a bond distance. At the same time I constrain seven atom coordinates during the entire optimization (this is ...
5
votes
1answer
704 views
How to use dispersion correction with TPSSh in Gaussian 16?
A colleague of mine suggested to use TPSSh as a functional. Since I am applying Grimme's D3 dispersion correction by default, I was surprised that it wasn't implemented in the standard density ...
3
votes
1answer
32 views
Automated Identification of Isomeric Relationship from 3D Structure?
Is there a software package that when given two sets of 3D structures can return the isomeric relationship between them? Even if it was only able to state that they are conformational isomers that ...
5
votes
1answer
114 views
How can I recognize aromatic rings in a connection table?
Given a connection table (that is, a list of atoms, their connectivities/bonds, and the type of bonds), how can I detect the presence of an aromatic ring?
For reference, the aromatic rings in the ...
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0answers
111 views
How to interpret Gaussian output for excited states?
I have calculated the excited energies for benzene in Gaussian. The output therefore was:
...
10
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0answers
280 views
Understanding two-electron integrals in Gaussian 09
I was comparing the two-electron integrals (electron repulsion integrals, ERI) printed by various well-established packages (Gaussian, GAMESS, Molpro etc.) and observed that Gaussian is the oddball in ...
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0answers
23 views
Gas Sensor Simulation
I'm looking for a graphical software to simulate a gas sensor mechanism. I thought "comsol multiphysics" could help me to determine the sensing mechanism of semiconductor gas sensor , but I didn't ...
3
votes
2answers
67 views
Is there a piece of software that can help me see the (hkl) planes in a crystal lattice?
I am doing research with calcium carbonate structures. I need a way in which I can familiarize myself with the lattice structure of calcium carbonate polymorphs, especially calcite.
I really struggle ...
1
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1answer
30 views
How to display ligands as ball and stick and macromolecules as cartoons (if protein) / rings (if nucleic acids) in Avogadro?
Avogadro has many good qualities but I can't seem to find a way to display ligands differently to macromolecules in the same view window. Frankly I can't seem to find a way to display any two things ...
0
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3answers
56 views
How to calculate number of each type of atom in a residue in PyMOL?
I have a 3D model of PDB 4UDC (dexamethasone bound to human glucocorticoid receptor), and I'd like to calculate how many atoms of each element are in the dexamethasone molecule (which has the residue ...
1
vote
0answers
63 views
How does the “sample type” selection on the MassHunter software for Agilent 7900 ICP-MS affect the quantitative results?
I'm new to using the instrument, and recently I have tried to measure Cr in both the eluent(1% nitric acid) and a method blank (also 1% nitric acid, but after it has gone through the entire analytical ...
4
votes
2answers
542 views
How do I make a ZMAT or XYZ file from scratch?
From a structure representation like the one below for Bacteriochlorophyll A, how do I make the ZMAT or XYZ file?
The closest similar question asked here was about converting a PDB entry into XYZ, but ...
4
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0answers
48 views
Chemistry write-ups in LaTex - is it worth drawing figures in LaTex? [closed]
Being an undergraduate chemistry student I have to write a significant amount of hand-ins e.g. lab reports. Up until now I've been using LaTex with mhchem for ...
1
vote
1answer
46 views
Is it possible to define the coordinates of an atom using other coordinates while optimizing in gaussian 16?
I know it is possible to fix the value of composite expressions using generalized internal coordinates (gic) in gaussian 16. But is it possible to assign that value to the coordinate of another atom.
...
5
votes
0answers
139 views
What computational methods are available for predicting nanoparticle structure?
I'm a quantum chemist, and nearly every system I've ever cared about has been studied by DFT. However, I am currently trying to model the surface interactions on a nanoparticle around 100 nm in ...
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votes
1answer
90 views
How to specify complete active spaces in the Dalton software package? [closed]
What do the numbers for specifying the inactive and active space of a Dalton calculation mean?
For example, I do not understand what the following numbers refer to:
...
10
votes
1answer
1k views
How to visualise the total electron density from a Gaussian 16 calculation?
I am trying to generate a 3D visualisation of the total electron density of a molecule. Using Gaussian 16, I have optimised this structure, with DFT, and formatted the resulting ...
1
vote
1answer
59 views
Library / function for computation of molecular mass / molecular weight in C
We are looking for a function to be used for computing the molecular mass / molecular weight / formula weight in C, either in a library or standalone. So far we have found the following ...
6
votes
1answer
268 views
Calculating the density matrix from a WFN file
I want to calculate the density for the $\ce{HCN}$ molecule. This molecule has 14 electrons and thus 7 occupied molecular orbitals. I have a .wfn file which ...
1
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0answers
81 views
Rendering software for publication
Does anyone know how I can render chemical structures of small organic molecules to look like the below images?
I have been looking around, and I cannot seem to find an answer. The closest lead I ...
