Questions tagged [software]
For questions pertaining to software used by chemists for professional or academic purposes.
301
questions
2
votes
0answers
32 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 ...
5
votes
1answer
62 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
48 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
28 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, ...
0
votes
0answers
26 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
140 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
73 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
62 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
22 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
49 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
votes
0answers
69 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
75 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
273 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
67 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 ...
8
votes
2answers
514 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
127 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
117 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
52 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 ...
5
votes
0answers
98 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
88 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
85 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
votes
0answers
166 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
50 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
votes
0answers
316 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 ...
5
votes
1answer
208 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
23 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
37 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 ...
7
votes
2answers
312 views
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
342 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
votes
0answers
36 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
53 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 ...
2
votes
0answers
122 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$$
where $w$ is an XC ...
2
votes
0answers
51 views
How to obtain spectroscopic constants Omega_e, Alpha_e, B_e, D_e and D_0 from centrifugal constants?
I need to compute a spectroscopic constants of $N_2^+$ states and I would like to do it using LEVEL16 software, due to its high interpolation flexibility.
But it seems, that LEVEL16 can only compute ...
2
votes
0answers
76 views
ApexTrack: peak tail looks like a shoulder
I'm trying to implement ApexTrack algorithm in my software by following the description written by Waters. But many chromatograms that I see have noticeable tailing of peaks: .
No matter what ...
4
votes
0answers
63 views
How can I save and read the CI vector during CASSCF calculations in Gaussian?
I have searched through the GAUSSIAN 16 manual and have not been able to solve these two related issues:
(1) I want to be able to save the CI vector and load it as an initial guess for a different ...
4
votes
0answers
131 views
How to get the second electron affinity of tellurium?
I need the value of the second electron affinity of Te, i.e. the energy change associated with the attachment of an electron to a $\ce{Te-}$ anion
$$\ce{Te- + e- -> Te^{2-}}$$
In the books (e.g. J. ...
2
votes
1answer
417 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
227 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?
-2
votes
1answer
621 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:
...
6
votes
1answer
108 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 ...
12
votes
2answers
190 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
764 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
83 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
votes
0answers
131 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
226 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
385 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
votes
0answers
67 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
votes
0answers
43 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 ...
-1
votes
1answer
108 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
443 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 ...
