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Questions tagged [software]

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

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Are there any molecular modeling programs that can build materials made up of three or more elements into a cylindrical shape?

I would like to build a material similar to what is in the image below. I have tried programs such as Material Studio, Quantum ATK, and VNL, but most of them can only do materials with 2 elements.
ABDULMUJEEB's user avatar
6 votes
2 answers
266 views

Consistent atom names PDB

Lets say you have two times the same molecule in PDB format. PDB1: ...
Mehdi Nellen's user avatar
6 votes
4 answers
2k views

Thermodynamic properties software

I am looking for a software (can be freeware or purchased) to look up water and steam thermodynamic properties (e.g. density, enthalpy, entropy) preferably a macro in excel. What do you use for this ...
l3win's user avatar
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6 votes
1 answer
1k views

What are the preferred IUPAC names of these two compounds?

In a recent homework assignment we are asked to give IUPAC name to the following two compounds: I am not asking this question for homework help -- for that purpose I got both names correct, to the ...
user2249675's user avatar
6 votes
1 answer
1k views

How to write an entire trajectory into a single PDB file?

I have a trajectory (few frames) that I want to stack together and build a single PDB. I thought either to use VMD or MDAnalysis library. With VMD if I do ...
0x90's user avatar
  • 924
6 votes
1 answer
7k views

How to construct a QST2 input file for Gaussian16 for multiple reactants and products?

I am attempting to determine the transition state structure for the following reaction using the QST2 method on Gaussian 16: $$\ce{CH3 + N -> HCN + H2 }$$ However, I am struggling to put together ...
pennypeat's user avatar
6 votes
1 answer
272 views

How would one construct a 3D model of a molecule based on the crystal structure of its salts?

Often crystal structures found online from past published crystallography experiments are of the salt of a molecule of biologic interest, as opposed to the freebase form of the molecule itself. For ...
Josh Pinto's user avatar
  • 2,461
6 votes
1 answer
6k 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 ...
urquiza's user avatar
  • 721
6 votes
1 answer
657 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 ...
thalsit's user avatar
  • 63
6 votes
2 answers
20k views

Free software to draw Newman projections

I need to draw Newman projection of a molecule. Particularly 1,2-dicloroethane rotamers, but have no idea if there is any program to do that kind of things. Do you know about some program available ...
user avatar
6 votes
1 answer
355 views

How do I run MP2 and/or CCSD-level hyperpolarizability calculations with GAMESS?

I have used GAMESS before for TDHF (RPA) / TDDFT level first hyperpolarizability ($\beta$) calculations. However, I cannot figure out how to calculate $\beta$ with MP2 and CCSD for comparative ...
ComputationalNovice's user avatar
6 votes
1 answer
160 views

How to calculate molar mass of (6)UO2+2D and (6)UO2OH+D?

For a hydrogeochemistry project, I want to calculate the molar masses of some compounds. I came across a problem when encountering species like (6)UO2+2D (aq) and <...
thymaro's user avatar
  • 173
6 votes
1 answer
816 views

How can I choose the right symmetry in CAS calculation using MOLCAS?

With $C_{2\mathrm{v}}$ symmetry and a closed shell configuration, how can I choose the occupation for each irreducible representation in the input file?
M. Obies's user avatar
  • 109
6 votes
1 answer
485 views

What does the ZZE tag in an Chemical Table file refer to?

I have a number of Chemical Table files which include a "M ZZE" tag in the properties block. For example, in Galactobuxin, I have: M ZZE 1 31 23 In ...
Jivlain's user avatar
  • 195
6 votes
1 answer
1k 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 ...
theozh's user avatar
  • 673
6 votes
0 answers
561 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 ...
Avishai Barnoy's user avatar
6 votes
0 answers
638 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: ...
theozh's user avatar
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6 votes
0 answers
899 views

Molecular visualization software for Raspberry Pi?

I've been using our lab's code MCMD on my Raspberry Pi for fun and exploratory purposes. I'm trying to find a VMD, Avogadro, Ovito, or other equivalent that is usable on Raspberry Pi, e.g. to view ....
khaverim's user avatar
  • 3,620
6 votes
0 answers
255 views

What are the essential arrows for entering chemical equations in text?

I'm the author of a custom chemistry keyboard on iOS. I am looking at improving the selection of Unicode arrows I can provide. When the device is a phone in portrait mode, I don't have a lot of extra ...
Glenn Howes's user avatar
6 votes
2 answers
2k views

How to make a CP2K input file with Avogadro?

I am trying to learn to work with CP2K and now need to make its input file. CP2K has kind of adaptor for Avogadro2 but not Avogadro ( I don't know what is the relation between them !). I also tried ...
Aug's user avatar
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5 votes
7 answers
17k views

Resources for learning Chemistry

Based on various other Stack exchange site (Mandarin Chinese, Russian and German), we adapt this project here for chemistry, since it's a great idea to have all kinds of resources in one place. This ...
5 votes
4 answers
3k views

Open Source tools to draw a set of 2d molecular graphs from sdf file

I have a sdf file for around 50 small-molecules for which I am doing structure-activity study. I would like to draw 2d graphs of all the molecules such that the image would fit into a single journal ...
DurgaDatta's user avatar
5 votes
3 answers
1k views

What software was used to create these organic reaction scheme figures?

I am aware that software such as ChemDraw, ChemDoodle or MarvinSketch can be used to draw skeletal formulas and the like. But what can I use to draw (in a similarly professional way) reaction schemes, ...
Nick_2440's user avatar
  • 253
5 votes
3 answers
5k 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): ...
TobiR's user avatar
  • 243
5 votes
1 answer
9k 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 ...
Seminom's user avatar
  • 69
5 votes
1 answer
415 views

What is the purpose of Gaussian, itself?

I have been doing some research into computational chemistry, having never looked into the area before, and have read about a popular, paid-for software "Gaussian", and free alternatives such as "...
Jacob's user avatar
  • 874
5 votes
2 answers
1k views

Counting valency of atoms, in a molecule with python

The documentation for the indigo module can be found here http://ggasoftware.com/opensource/indigo/api#inputoutput So for instance if I have a molecule object for some SMILES string, e.g. ...
Freeman's user avatar
  • 233
5 votes
2 answers
6k views

ChemDraw: Automatic Caption with Number for Molecules

When working on some reaction schemes in ChemDraw, I sometimes forget to add text/captions with numbering and align it with my molecules before placing all the molecules in a reaction scheme and ...
Eljee's user avatar
  • 858
5 votes
1 answer
329 views

How to compute the electronic energy reported by Gaussian from the AlphaOrbitalEnergies?

I followed the instructions on Wolfram Language & System Documentation Center — FCHK (.fchk) to analyze the *.fchk file. I ran an energy calculation with ...
mostafa100000's user avatar
5 votes
1 answer
372 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 ...
RMurphy's user avatar
  • 151
5 votes
2 answers
344 views

Unix/MobaXterm Project Assistence (Knowing the Error in my Output File)

I'm a student and I recieved a project in which I am supposed to simulate a transition state in an $\mathrm{S_N2}$ reaction. The first instruction in this project is to use a benchmark reaction in ...
H B's user avatar
  • 79
5 votes
1 answer
1k views

Software for visualizing molecular force vectors

I would like to visualize molecular normal modes as vectors sitting on each atom, and not as actual vibrations. I am able to do this, in part, with Molden by copying in the vector into a file readable ...
Yoda's user avatar
  • 4,743
5 votes
2 answers
800 views

Free software for calculating the net charge of an amino acid as a function of pH?

Does a free software for calculating the net charge of amino acids as a function of pH exist?
Confused's user avatar
  • 169
5 votes
1 answer
252 views

Azathioprine CIF data file rendering problem in Accelrys

I have been working on a CIF data file based on experimental data [1] (free full text isn't available, but the page 2 with the experiment details can be found in the free preview provided by Springer)....
Josh Pinto's user avatar
  • 2,461
5 votes
2 answers
2k views

Which Chemical Database Software Are Available?

By chemical database software I mean software with similar functionalities to Instant JChem in that they have a large database of different compounds and have the basic capabilities you, or at least I ...
Josh Pinto's user avatar
  • 2,461
5 votes
1 answer
150 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 ...
Alex I's user avatar
  • 283
5 votes
2 answers
1k 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?
Cloud Chem's user avatar
5 votes
1 answer
2k views

Convert CIF file to SDF file using free Linux-compatible software other than Avogadro or OpenBabel?

I am trying to convert http://crystallography.net/cod/2236556.cif to a file that I can open in Avogadro without some bonds disappearing. See this crystal structure is of tianeptine hydrochloride, yet ...
Josh Pinto's user avatar
  • 2,461
5 votes
1 answer
624 views

Why Gaussian soft (STO-3G) causes error for Helium anion?

Software: G09.Rev.D.01 =======gjf-file====== ...
Sergio's user avatar
  • 925
5 votes
1 answer
48 views

How to avoid the appearance of extra hydrogens from lattice packing of PDB file?

I'm struggling with a pdb file of a unit cell that has a $\ce{CH3}$ which becomes a $\ce{CH6}$ when some software performs replication transformations. I've tried pack it with Avogadro and Mercury. ...
thiago's user avatar
  • 51
5 votes
1 answer
261 views

Extracting "Crystal Radii" from a CIF file

I'm currently downloading .cif files from various online databases and using openbabel to convert the fractional coordinates that are in the .cif files into .xyz files. The typical output will look ...
mike van der naald's user avatar
5 votes
1 answer
143 views

Are there computer searches for new theoretical minerals in a similar vein to Folding@Home or SETI@Home?

As a surprise gift to a friend I would like to discover a new theoretical mineral and have it named after them. I have some understanding that not all minerals have been discovered, and some minerals ...
Ross Snider's user avatar
5 votes
2 answers
5k 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 ...
user1271772's user avatar
  • 1,452
5 votes
1 answer
423 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 ...
derek correa's user avatar
5 votes
1 answer
917 views

How to get force constants in internal coordinates in Gaussian?

I have tried quite a few different ways to get Gaussian to print the force constants in internal coordinates. If the size of the molecule is small then it prints both the internal hessian and ...
ace_101's user avatar
  • 146
5 votes
1 answer
218 views

Relaxed scan of Cp-M torsion angles of piano stool compounds

As part of a conformation analysis of a library of piano stool complexes to find global minima and TS, a relaxed scan where the legs of the piano stool complex rotated about the Cp-M bond need to be ...
Secret's user avatar
  • 698
5 votes
1 answer
894 views

Defining the Turbomole named BP86 functional in Gaussian [closed]

According to Turbomole, the BP86 density functional has the following definition: $$ \mathrm{Exchange = LDA + B88\\ Correlation = LDA(VWN(V)) + P86} $$ What is the equivalent definition in Gaussian ...
fff's user avatar
  • 61
5 votes
1 answer
2k 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 ...
Persian_Gulf's user avatar
5 votes
2 answers
190 views

How would you add saccharide residue information to PDB files?

I have multiple PDB files containing a single molecules of polysaccharides, with a single chain and a long list of all the atoms -they are not divided by residue. The PDB files were created from ...
babu's user avatar
  • 51
5 votes
1 answer
512 views

Modified DNA bases in Pymol and Coot

When using Pymol or Coot molecular visualization software to solve x-ray crystallography structures, how can I mutate a cytosine to a 5-methylcytosine?
Rachel W's user avatar

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