Questions tagged [software]

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

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51
votes
1answer
1k views

How can I update a map/mesh and coordinates in a PyMol session file?

I have a PyMol session file I was using to create my figures. It contains a protein and ligand broken into several groups of atoms with a fair bit of overlap. There are also a few meshes built from ...
36
votes
5answers
11k views

Generating neat orbitals/surfaces from molden/wfn-files

I usually use Gaussian/GaussView and don't have to bother with other programs as I think that GaussView is capable of producing nice orbital/surface pictures like this one of one of uracil's Kohn-Sham-...
28
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4answers
1k views

How do Quantum Software Packages Work?

If one wants to calculate a moderate size Alkane (with say 10-15 Carbons , assuming 100 electrons , with Restricted Hartree Fock based methods) we can simply say that electron-electron part will be $...
26
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4answers
3k views

What software can calculate aqueous solution equilibria?

What software is available out there to calculate the equilibrium in a set of reactions in aqueous solution? In particular, I'm interested in software general enough to simulate things like titration ...
26
votes
2answers
1k views

Equivalent of Szabo and Ostlund book for DFT

Szabo and Ostlund book Modern quantum chemistry [1] is extremely useful to understand Hartree-Fock and post-Hartree-Fock methods. Not only it explains the theory behind such methods, but it is also ...
25
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1answer
2k views

What software is used to generate the PDB molecule of the month images?

What software does the PDB use to generate these "cel-shaded" protein models with outlines around foreground atoms? (Leptin: May 2012 Molecule of the Month by David Goodsell)
23
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4answers
232k views

How do I type a simple chemical equation in Microsoft Word?

How do I type a simple chemical equation in Microsoft Word? I can do subscripts, but long arrows are more difficult. I can't get them to align with the text. Also, I can't figure out how to put a ...
23
votes
1answer
612 views

Structure that breaks InChI

I am currently testing a piece of software that generates the InChI for a given structure. I also want to test error situations as end users will also deliver the mol files that will be used as input ...
22
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3answers
9k views

What open-source software can produce 3D PDF representation of molecules?

Most of the existing software I know (like VMD or Pymol) say that they can be used to create PDF files with 3D representations of molecules: actual 3D models, which you can rotate inside the Adobe ...
21
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1answer
485 views

Is the Springborg 6D phase space model used in modern molecular orbital modeling?

In a series of papers in the early 1980s, Michael Springborg explored an interpretation of the Wigner phase space function as an electron density in a six-dimensional $(q,p)$ phase space. He applied ...
18
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1answer
9k views

Creating energy profile diagrams for publication

Is there automated software to create energy profile diagrams like the ones below? One could use something like Illustrator or Inkscape, but they aren't automated, are expensive (Illustrator), are ...
17
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1answer
13k views

How can I draw metallocenes in ChemDraw?

How can I properly draw the structure of metallocenes (e.g. ferrocene) and similar sandwich compounds in ChemDraw? In particular, two problems cannot be solved with the usual workflow when building a ...
16
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4answers
2k views

Easiest way (software) to visualize charge density from an .xyz file with point-charges?

I have an .xyz file which contains partial charges calculated by a Quantum-Chemistry software (NWChem). The system looks like this, here I show the partial charges calculated from the electrostatic ...
16
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2answers
601 views

How do I create a spreadsheet containing the coordinates and predicted bond angles, molecular properties, torsion properties, etc of a molecule?

On a previous answer here (https://chemistry.stackexchange.com/a/30841/876) I was informed in the comments that OpenBabel & Python terminal could be used to print the data contained in the ...
15
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2answers
18k views

How to find a transition state for an electrophilic addition with Gaussian and map the reaction pathway?

I aim for two things with this post – on the one hand to produce a manual for other people to use, but also to verify what I obtained via searching, asking a more experienced user as well as receiving ...
15
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2answers
2k views

Software for viewing a structure and altering bond angles

Does anyone know of any good software that would allow me to view the structure of a compound while also allowing me to change the bond angles in the structure (and give me numeric values for those ...
14
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2answers
957 views

How should elements be colored? And how many bonds does an atom have?

I'm working on my own 3D molecule viewer for my AP Chem class. So far everything's going together nicely. There's a couple of things I'm not sure about though... Is there a certain rule of thumb or ...
14
votes
1answer
850 views

Is Orca wrongly breaking bonds? Why can it only optimize the molecule with COPT activated?

I would like to ask for help in using Orca (v. 4.0.0) for conducting a simple optimization. First I have this structure (primarily optimized using MMFF94s force field on Avogadro): Thus I tried to ...
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 ...
13
votes
1answer
3k 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 ...
12
votes
1answer
2k views

How to simulate chemical reactions in GAMESS?

I am rather newb in GAMESS field but finally, learned to make input files for most molecular simulations and could even use TD-DFT for excited states (special thanks to Geoff Hutchison for his help). ...
12
votes
1answer
387 views

Trying to understand SMILES(?) patterns

In the example calculation from the conformer search package fafoom is a mysterious pattern that I'd like to understand. The SMILES code of the given example structure is: ...
12
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2answers
251 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 ...
12
votes
1answer
400 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 ...
12
votes
1answer
1k views

Definition of the B3LYP functional in common QC programs

I wanted to use custom functionals with Gaussian and came up with some interesting definitions of the B3LYP functional within Gaussian, Orca and Turbomole, ... $$\small\begin{array}{lcccccc} \hline ...
11
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3answers
10k views

Program that simulates basic reactions in organic chemistry

To explain - a friend and I have been working on a program that would allow you to draw organic molecules, indicate the conditions, and predict the products. This would be primarily aimed at basic, ...
11
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0answers
84 views

Is there a structured data source containing information on the World Health Organisation's Stability Testing Policies?

Hoping to automate some product testing guidance software, I've been attempting to find a (hopefully live, up-to-date) Database, Web-service, or other structured data source containing the ...
10
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2answers
2k views

Methods for Determining Partial Charges

I want to run classical molecular dynamics simulations of a periodically replicated surface (rutile $\ce{TiO2}$ with grooves). In order to do so, I first need to solve for the partial charges residing ...
10
votes
2answers
667 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, ...
10
votes
3answers
258 views

How can I perform structure alignment on an inorganic species?

I'm attempting to perform atomistic optimal structure alignment on an inorganic species. Can anyone point me in the right direction to software or a technique for performing this? There exists a wide ...
10
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0answers
636 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 ...
9
votes
5answers
1k views

How can I calculate the charge distribution of a water molecule?

I would like to obtain the 3D charge density of a water molecule for plotting purposes (i.e. not necessarily super-accurate). I know this is a tough problem, but I'd like to give it a try. Since I'm ...
9
votes
4answers
717 views

What free software exists to view molecule pictures within a file explorer?

I am testing my small api library that generates lots of chemical files such as MOL and SDF. I was wondering if there is a software that can show me the pictures of chemical structures inside each ...
9
votes
3answers
1k views

How to add hydrogens to a crystal structure?

PDB protein crystal structures most of the time lack hydrogen atoms. Usually I use PyMOL (h_add) but it does not always seem to be giving the correct result. What ...
9
votes
3answers
11k views

How to convert SPC files to ASCII without original spectroscopy software?

IR and Raman spectroscopy are typically saved in *.SPC files (chemical/x-galactic-spc), which are binary files. Collected data is save to SPC files by default, but ...
9
votes
3answers
1k views

InChIKey generation from InChI

I am trying to find some good resources to understand generation of InChIKeys from the InChI. There seems to be no resource available online. I have gone through the Wikipedia article for InChI, but ...
9
votes
1answer
2k views

What are GAMESS and Gaussian?

I've been seeing a lot of GAMESS and Gaussian questions around here, and most of them seem very hard to answer. I extrapolated that they might be some sort of Chemistry programs, but what do they do ...
9
votes
3answers
770 views

Conversion of Hessian from internal coordinates to cartesian coordinates

I have performed a CASPT2 frequency calculation using the MOLCAS8 program package. I need the full Cartesian Hessian matrix as input for a subsequent program package. MOLCAS8 performs CASPT2 ...
9
votes
1answer
595 views

What are simple applications of Monte Carlo simulations in chemistry, that can be done in Matlab?

I am trying to learn simulation myself and I have installed Matlab on my machine for that purpose. In web I have gone through some of the basics of Monte Carlo simulation, but I am unable to find a ...
9
votes
1answer
575 views

Does MOPAC allows calculation of Standard Enthalpy of reaction in this way?

I am using MOPAC2016 to calculate $\Delta H^\circ_\mathrm{r}$ (and then $\Delta G^\circ_\mathrm{r}$) for a reaction in aqueous phase, at $\pu{298 K}$. I will explain how, and then the question. ...
9
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1answer
1k views

How to perform molecular dynamics simulations of charged systems?

The GROMACS official documentation (see here) states that a system with non-zero total charge will yield an error: System has non-zero total charge Notifies you that counter-ions may be required for ...
9
votes
1answer
162 views

How to color bonds by the strain?

I need to create a figure of a molecule in which the bonds are colored in a RGB scale according to the values read from a data file. The data file contains, for example, the increase or decrease in ...
9
votes
2answers
913 views

NMR calculations with NWChem quantum chemistry program

I tried experimenting with some ab initio NMR calculations using the NWChem program. I used quinuclidine as a simple test case. The input file was: ...
9
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1answer
368 views

Learning chemistry with software?

I'm interested in learning organic chemistry, and am following a text (Organic Chemistry by Clayden) and an online course. I also have access to ChemBio3D. I feel as though the way chemistry is ...
8
votes
2answers
4k views

Extract all structures of Gaussian 09 molecular dynamics calculation using babel?

Is there a way to easily extract all the structures and energies from an ADMP calculation done in Gaussian 09? GaussView can plot them but not export them in a useful way and babel just gives me the ...
8
votes
2answers
1k views

How to connect structures in Avogadro at certain angles?

I am working with this carbon nano-structure in Avogadro and the junction between my two nano-structures I try to join never seems to be aligned well. It always seems to be off kilter, which is most ...
8
votes
1answer
792 views

How to specify a different isotope in the ORCA quantum chemistry program?

I would like to carry out a calculation using deuterium instead of hydrogen. I tried the following ORCA input file: ...
8
votes
1answer
2k views

How to obtain the radial probability distribution function from a quantum chemical calculation?

In the book "Quantum Chemistry" by Ira Levine I found a plot of the radial probability distribution function of argon: The figure appears in the context of the following section: Electron ...
8
votes
2answers
454 views

Reliable automatic addition of hydrogens and charge assignment to small molecules at given pH?

I have some PDB structures of small molecules with missing hydrogens. Is there a software available that places missing hydrogens and assigns a charge to the molecule that is reliable? I am looking ...
8
votes
1answer
3k views

How does one export a PDB structure to SVG?

This question is one that I'm wondering whether it belongs here or on Graphic Design SE. All I want is some software that can export a PDB structure of a protein (displayed in ribbons style) or DNA ...

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