Stack Exchange Network

Stack Exchange network consists of 175 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers.

Visit Stack Exchange

Questions tagged [software]

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

0
votes
0answers
11 views

Convert CONTCAR to .cif file

i got a CONTCAR file and like to convert to .cif file. Could someone help me to with any source code to convert this? Thanks in Advance !!
-4
votes
0answers
15 views

Creating simulations online to get a better intutive ideas about abstract topics in chemistry [on hold]

As a Lecturer in Chemistry, I have used ready made simulations for students by https://phet.colorado.edu/en/simulations/category/chemistry where it deals with performing some online experiments to get ...
-2
votes
0answers
29 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
21 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 ...
10
votes
2answers
101 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
364 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
46 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
57 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
102 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
93 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
35 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
36 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
44 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
88 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
63 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
votes
1answer
39 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
79 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
45 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
50 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
80 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
80 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
60 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 ...
3
votes
1answer
439 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
30 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
105 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 ...
1
vote
0answers
76 views

How to interpret Gaussian output for excited states?

I have calculated the excited energies for benzene in Gaussian. The output therefore was: ...
8
votes
0answers
192 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 ...
0
votes
0answers
19 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
60 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
vote
1answer
27 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
votes
3answers
47 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
48 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
386 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 ...
3
votes
0answers
45 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 ...
-4
votes
1answer
82 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
249 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
vote
0answers
76 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 ...
3
votes
2answers
466 views

Molpro wavefunction symmetry specification

I'm beginning to use Molpro software for some computations. But I got completely confused by its description of specification of wavefunction symmetry. It tells us, that the symmetry of wavefunction ...
6
votes
1answer
296 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 ...
2
votes
0answers
41 views

Setting to basis set for electron transfer in type II CdS/TiO2 heterostructre for PYXAID package

I am studying electron injection from $\ce{CdS}$ into $\ce{TiO2}$ using NAMD approach. Now I'm using pyxaid package. Would be possible someone kindly help me with construction of basis set for this ...
4
votes
0answers
334 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 ....
1
vote
1answer
68 views

How to unify all the subunits in a PDB file?

A PDB may contain a TER token. For example, hemoglobin has 4 subunits separated by a TER identifier. If we take hemoglobin's ...
4
votes
2answers
193 views

How to determine if two calibration curves are parallel, within 5%

I have complex matrices and I need to make sure the matrix does not affect the measurement of my analyte. To do that, I need to prepare samples of my analyte in a solvent and of the matrix reinforced ...
2
votes
0answers
172 views

3D similarity search software [closed]

What software / webservice can one use to find a compound that has similar 3D structure/dimension to another compound? eg. say we are tying to find a 'better' version of atropine, so naturally we try ...
6
votes
1answer
151 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 ...
7
votes
1answer
352 views

How do I perform a partial optimisation in GAMESS?

Sometimes it is necessary to perform a partial optimisation of a molecule, i.e. keeping certain variables constant. One example might be to pre-optimise a transition state, taking advantage of not ...