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Questions tagged [software]

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

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51 votes
1 answer
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 ...
Nick T's user avatar
  • 2,563
38 votes
5 answers
15k 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-...
pH13 - Yet another Philipp's user avatar
28 votes
4 answers
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 the electron-electron part will be $...
Aug's user avatar
  • 2,141
26 votes
4 answers
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 ...
F'x's user avatar
  • 23.9k
26 votes
2 answers
2k 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 ...
user avatar
25 votes
4 answers
244k 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 ...
Sualeh Fatehi's user avatar
25 votes
1 answer
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)
Nick T's user avatar
  • 2,563
23 votes
3 answers
10k 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 ...
F'x's user avatar
  • 23.9k
23 votes
1 answer
771 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 ...
cheffe's user avatar
  • 365
22 votes
1 answer
578 views

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

In various papers written in the 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 it ...
Terry Bollinger's user avatar
19 votes
1 answer
14k 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 ...
pentavalentcarbon's user avatar
18 votes
1 answer
22k 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 ...
user avatar
16 votes
4 answers
3k 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 ...
khaverim's user avatar
  • 3,610
16 votes
2 answers
21k 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 ...
DetlevCM's user avatar
  • 555
16 votes
2 answers
689 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 ...
Josh Pinto's user avatar
  • 2,461
15 votes
2 answers
1k 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 ...
Chance Leachman's user avatar
15 votes
2 answers
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 ...
Melanie Shebel's user avatar
15 votes
2 answers
449 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 ...
DC Y's user avatar
  • 373
14 votes
3 answers
3k 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 ...
Ruben J.'s user avatar
  • 181
14 votes
1 answer
1k 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 ...
Manoel Barrionuevo's user avatar
14 votes
1 answer
2k 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 ...
pH13 - Yet another Philipp's user avatar
13 votes
1 answer
6k 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 ...
C. Walsh's user avatar
  • 141
12 votes
1 answer
3k views

How to simulate chemical reactions in GAMESS?

I am rather a newb in the 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 ...
Aug's user avatar
  • 2,141
12 votes
1 answer
448 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: ...
pH13 - Yet another Philipp's user avatar
12 votes
1 answer
837 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 ...
andselisk's user avatar
  • 38k
12 votes
0 answers
1k 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 ...
DC Y's user avatar
  • 373
12 votes
0 answers
92 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 ...
user32052's user avatar
  • 121
11 votes
3 answers
11k 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, ...
Dan Oberlam's user avatar
11 votes
2 answers
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 ...
commanderdata's user avatar
11 votes
2 answers
1k 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, ...
jheindel's user avatar
  • 13.1k
10 votes
5 answers
2k 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 ...
uhoh's user avatar
  • 5,822
10 votes
4 answers
979 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 ...
user6834's user avatar
  • 225
10 votes
1 answer
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 ...
Asker123's user avatar
  • 3,050
10 votes
2 answers
5k 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 ...
DSVA's user avatar
  • 5,782
10 votes
1 answer
895 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. ...
user avatar
10 votes
3 answers
269 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 ...
Richard Terrett's user avatar
10 votes
1 answer
4k 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 ...
Buttonwood's user avatar
  • 30.1k
10 votes
1 answer
493 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 ...
ccITguy's user avatar
  • 117
9 votes
2 answers
383 views

Software to draw one-dimensional PES including vibrational energy levels

I am trying to represent the difference between the an anharmonic and harmonic treatment of vibrations. The easiest way to do this is to present an example of a harmonic and anharmonic potential ...
isolated matrix's user avatar
9 votes
3 answers
3k 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 ...
Mehdi Nellen's user avatar
9 votes
3 answers
14k 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 ...
Sparkler's user avatar
  • 4,275
9 votes
3 answers
2k 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 ...
LifeIsGood's user avatar
9 votes
1 answer
5k 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 ...
Josh Pinto's user avatar
  • 2,461
9 votes
3 answers
1k 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 ...
mrnicegyu11's user avatar
9 votes
1 answer
2k views

How to save the force on a molecule in GROMACS?

I am a new student of molecular dynamics. I have started using GROMACS a month ago. I have a small box of 8192 molecules each with 3 atoms. I froze the last molecule and ran the simulation. I even ...
subn's user avatar
  • 91
9 votes
1 answer
631 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 ...
Eka's user avatar
  • 2,768
9 votes
1 answer
2k 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 ...
logical x 2's user avatar
  • 2,794
9 votes
1 answer
278 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 ...
Max Pinheiro's user avatar
9 votes
3 answers
1k 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: ...
logical x 2's user avatar
  • 2,794
9 votes
1 answer
424 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 ...
user4779's user avatar
  • 691

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