Questions tagged [software]

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

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1 answer
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How to draw endo-bicyclo[2.2.1]hept-5-ene-2,3-dicarboxylic anhydride on ChemDraw?

I'm struggling to draw endo-bicyclo[2.2.1]hept-5-ene-2,3-dicarboxylic anhydride on ChemDraw. I currently have this: How can I draw it in the chair conformation side on view? I know what it is ...
avogadros_pupil's user avatar
0 votes
0 answers
41 views

15N NMR simulation with orca software

I would like to simulate J(15N-1H) couplings with orca. By default, the software uses the 14N isotope for NMR nitrogen simulation. In the program, in the xyz input, I added M 15 on the line of the N ...
emmanuel C.'s user avatar
0 votes
0 answers
45 views

XRD experiment: how to interpret data and solve crystal structure from 2theta vs intensity values

I have just performed an XRD (X ray diffraction) experiment (powder), but the XRD machine I have used is not able to describe crystal data, I have $2\theta$ and intensity in arbitrary units in a UXD ...
Ștefan Dumitrescu's user avatar
0 votes
0 answers
62 views

HOMO and LUMO energy levels diagrams

Good time of day. I want to draw the same beautiful pictures in my work as I will attach below taking from some articles. Are there any programms or scripts which can do this? I would be glad if ...
UserIn's user avatar
  • 1
0 votes
0 answers
19 views

Automatically extracting SMILES of sub-group of larger SMILES structure?

Is there any software tool that can automatically extract SMILES of fatty acid legs of phospholipids if the SMILES of the parent lipid is given? Or any tool that can do it in InChI ? Any advice will ...
user1776194's user avatar
1 vote
0 answers
62 views

"Is there any library in Python or software for analyzing raw chromatography data?"

I have taken the data directly from the FID sensor using a DAQ, so I have the chromatography data in this format: (2 data colummns in a txt file) (18000 rows) Time (s) Intensity (V) 0.00367___0.0008 ...
user138375's user avatar
1 vote
1 answer
150 views

Programs to view or convert unformatted Mass Spec data

I've been give mass spec data in very simple format .txt files. Each file is two columns, m/z and intensity. There is no header or anything. Are there any programs that can read this file? Or how can ...
J.R.'s user avatar
  • 21
0 votes
0 answers
23 views

Free alternatives to ChemDraw [duplicate]

My school doesn't offer me a ChemDraw license and I need to be able to draw quite complex chemical structures (e.g. porphyrins). This is why I am interested in some good free alternatives to ChemDraw. ...
ChemistryGeek's user avatar
1 vote
0 answers
61 views

Hartree-Fock calculations of the states of Nitrogen molecule ion

I was reading the third chapter of "Modern Quantum Chemistry" by A. Szabo and N. Ostlund about HF calculations, and in the end of the chapter it shows as an example a calculation on $\ce{N2}$...
AlfredV's user avatar
  • 461
3 votes
1 answer
260 views

Problem adding non-polar hydrogens whilst converting from pdbqt to pdb

I'm using OpenBabel 3.1.1 and the Python to C++ bindings to load pdbqt files and convert them to pdb with explicit hydrogens. Unfortunately, I can't add nonpolar hydrogens using OpenBabel. I can do ...
Anthony Nash's user avatar
9 votes
2 answers
351 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
-2 votes
1 answer
3k views

How to make bonds thicker in ChemDraw?

I often see molecules depicted using ChemDraw with all or selected bonds visibly thicker than those used with the style defined with ACS-1996 template. For example, see the PDF handouts for Baran's ...
Lanagan's user avatar
2 votes
1 answer
158 views

Open MSDS (GHS/CLP) database API by CAS#

I am looking for an open API to a database that provides GHS/CLP classifications. I am aware this is a duplicate, however the post in question never provided an answer since, as far as I can tell ...
Julien's user avatar
  • 37
1 vote
0 answers
150 views

Gibbs Free Energy for solvation using Gaussian09

I am trying to compute the $\Delta G$ for the solvation of a molecule using the continuum dielectric model in Gaussian09. Following the recomendation in the manual of the software, I am using the SMD (...
AlfredV's user avatar
  • 461
1 vote
0 answers
22 views

Software for running dynamics simulation of polymeric and mixed biomaterial (e.g hydrogels)

I was working on the development of a soft solid hydrogel having polymeric chains and molecules of different compounds dissolved in Phosphate Buffered Saline solution. There is a sub-study regarding ...
Syed Hasan Sarwar's user avatar
0 votes
0 answers
98 views

Input file details for rigid PES scan

I have a planar molecule and a hydrogen atom. I wish to perform single point energy calculation for different configurations of this system where I would place the hydrogen at a certain distance away ...
Arun's user avatar
  • 1
-3 votes
1 answer
237 views

How to convert molecule structure to 3D PyTorch tensors for CNN? [closed]

I want to try convolutional neural networks for drugs classification. I use PyTorch for 3D CNN implementation. Is there a way to obtain 3D tensors from SMILES or SDF/PDB structures?
sigma's user avatar
  • 1
3 votes
1 answer
225 views

Python implementation of the Lilly Medchem Rules code? [closed]

As the title suggests, I am looking for a Python implementation of the Lilly filter from the paper: https://pubs.acs.org/doi/full/10.1021/jm301008n. The shared code on GitHub (https://github.com/...
mac179's user avatar
  • 319
0 votes
0 answers
47 views

How can I calculate average interatomic distance between all identical elements in supercell?

Good afternoon! Maybe someone came across, I want to know the average interatomic distance between all identical elements in some supercell. In Vesta or a similar program, it shows only one piece at a ...
Ryba4ok's user avatar
1 vote
0 answers
1k views

Full list of CAS numbers?

I'm trying to find a full list of CAS Registry Numbers, but it looks like it's not in open access. Is it a proprietary database that can't be downloaded easily?
Stefan Smirnov's user avatar
1 vote
1 answer
427 views

Does the 3D structure generated with MolView violate the wedge-dash rules of "above/below the plane"?

I've been taught that in a wedge-dash diagram, the wedge represents a bond above the plane of the paper, and the dash represents a bond below the plane. Accordingly, I expected the structure of this ...
Righter's user avatar
  • 304
2 votes
1 answer
223 views

Creating custom spectra graphs

I wanted to make a few custom spectra graphs for some homework questions I'm assigning. The issue is that the Education Board issued datasheets do not reflect online images. They often say that bonds ...
John Hon's user avatar
  • 1,566
4 votes
0 answers
239 views

Is There a Problem with the Assignment of Stereochemical Descriptors by ChemDraw in Select Examples?

While using ChemDraw Professional 21.0.0.28 to construct some cyclic allenes and rotationally restricted biphenyls, I came across anomalous assignments of stereochemistry. [For the latest version of ...
user55119's user avatar
  • 16.6k
5 votes
1 answer
325 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
1 vote
1 answer
141 views

Crystal packing prediction for simple organic molecules?

Is it yet possible to predict a simple organic molecule's crystal structure or how the molecules arrange in a crystal without diffraction measurements? By crystal structure I mean, how would molecules ...
kpeteL's user avatar
  • 53
1 vote
0 answers
62 views

Any Open-Source, Free Software That Can Be Used to Computationally Calculate Binding Affinity Between Two Molecules? [closed]

There are programs out there which calculate the binding affinity between a ligand and a target protein (Autodock 4, Autodock Vina, Chimera... etc). Is there any analogous program that can be used to ...
Mas's user avatar
  • 447
1 vote
1 answer
587 views

Troubleshooting an AutoDock Vina error on Chimera: “Could not find an atomic number for Hn Hn”

After minimizing a ligand (prepared with MarvinSketch) and preparing a target enzyme to dock said ligand onto (collected from RCSP PDB — 5DGN (Crystal structure of human FPPS in complex with compound ...
Mas's user avatar
  • 447
6 votes
1 answer
5k 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
  • 711
0 votes
0 answers
285 views

Software for drawing biomolecules (with functional groups abbreviated)

I'm sorry if this is OT, but I find myself slowly going insane trying to draw common biomolecules such as Acetyl Coenzym A. The thing is, I just want to draw the acetyl part and then link that to a ...
Magnus's user avatar
  • 161
4 votes
1 answer
216 views

Computational determination of the diagram of molecular orbitals of a polyatomic chemical species

A diagram of molecular orbitals for $\ce{H2O}$ would be as follows: The above diagram has been constructed qualitatively following the steps that I have been instructed in various classes on this ...
Carlos's user avatar
  • 607
1 vote
1 answer
67 views

How do I expand a selection in Jmol to include entire residues?

I know how to select by distance in Jmol: select within(5, ATP) This selects atoms that are within 5 Angstroms of ATP residues. How do I expand the selection to include the entire residues of the ...
Karsten's user avatar
  • 40.2k
3 votes
1 answer
275 views

Quantum chemistry Python package to solve the Coupled-Perturbed Hartree–Fock equations

Two of the most well-known Python quantum chemistry pakcages, PySCF and Psi4, can solve the Hartree–Fock equations. However, I am interested in finding analytic derivatives of the electron integrals: $...
Jack Ceroni's user avatar
0 votes
1 answer
301 views

How to Build Hydrogen Atoms in MOE using SVL

I'm working on automating a process in MOE using SVL commands. I've got pretty much everything worked out, except I can't seem to find anything for building hydrogen atoms using an SVL command (...
QuantumDebris's user avatar
2 votes
1 answer
923 views

Converting a CIF file to a .com or .gjf file

I would like to perform DFT calculations and extract atom coordinates for calculations in Gaussian. I am using Mercury and have been able to isolate the atoms that I am interested in simulating. ...
Han Den's user avatar
  • 21
1 vote
0 answers
42 views

How can I save an EEM file on a Fluoromax4?

I'm trying to run excitation-emission matrices on some water samples, but I'm running into some software issues that the manuals aren't helpful for. In order to use R studio to extract my data, I need ...
dogman's user avatar
  • 61
1 vote
0 answers
29 views

small negative frequencies in DF T optimizations with organic molecules containing CF3 groups [duplicate]

When optimizing by DFT medium-sized organic molecules containing aromatic CF3 groups (for example, adducts involving takemoto's catalyst), the frequency calculation on optimized structures have always ...
saiwa's user avatar
  • 31
6 votes
1 answer
264 views

Discrepancy when calulating mol weights with ChemSketch and Python RDKit

I am an IT guy with little knowledge of Chemistry, so please bear with me... For context: I am working with a system that has a lot of structures, their .mol files ...
buddemat's user avatar
  • 235
5 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
  • 663
1 vote
0 answers
44 views

Is there a computer program capable of showing protein conformational changes based on pH?

As it is known, changes in pH change the attractions between the groups in the side chains of the protein. Acidification can, for example, cause protonation of the $\ce{COO-}$ end to $\ce{COOH},$ ...
RoyBatty's user avatar
  • 111
2 votes
1 answer
3k views

Titration curve equation/function

How can I create a graph of a titration curve (acid-base, strong or weak, not something specific), with an equation or a function. In other words, what is the equation that describes such a curve that ...
MariosA's user avatar
  • 39
7 votes
1 answer
994 views

ORCA: How to plot an adiabatic potential in dihydrogen H2 molecule?

I stared to study ORCA, and I try to obtain classical results for dihydrogen as for example. I need to get a starting point to understand what needs to be done. So, How to plot an adiabatic potential ...
Sergio's user avatar
  • 915
0 votes
2 answers
890 views

How to get the coordinates of β12 borophene and χ3 borophene?

Can someone tell me how to draw the β12 borophen and χ3 borophene in Materials Studio or any other software? I've just started my project work, and I'm a beginner in this field. I have searched for ...
aritraroy24's user avatar
0 votes
1 answer
2k views

How to draw "box"/square arrows in Chemdraw Prime 16.0?

I want to draw arrows like the one in the figure shown (with reagent a beside it) in ChemDraw 16.0 What is the best way to go about this? I couldn't find anything like it in the arrow options in ...
Marcy Melvin's user avatar
7 votes
1 answer
9k views

ChemDraw: how to change the default aromatic ring style for drawing from SMILES

I'm a beginner at ChemDraw. I'd like to draw a molecule from SMILES and the ring bond should be drawn like the left image: In my case, my image is drawn like the right image. Is there any method to ...
Hyunseung Kim's user avatar
2 votes
0 answers
38 views

CP2K Spherical Cell

I'm trying to run a gas phase cluster calculation in CP2K. I want to create an outside force to constrain water molecules that are in the simulation within a radius of a central ion. I want to create ...
dtg67's user avatar
  • 41
7 votes
1 answer
310 views

Using RDKit to determine "nonring, nonterminal atoms"

I am a non-chemist using RDKit to determine the number of "nonring, nonterminal atoms" in a molecule. I can't find anything in the RDKit documentation that helps with "nonterminal"....
user118967's user avatar
8 votes
1 answer
736 views

Using RDKit to count "RR, the number of rigid single or fused ring systems in the molecule"

I am a computer scientist, not a chemist, working with RDKit. I need to compute something described to me as "RR, the number of rigid single or fused ring systems in the molecule." I know I ...
user118967's user avatar
5 votes
1 answer
140 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
-1 votes
1 answer
251 views

Install MOLDEN in MACOS Big Surf [closed]

I'm trying to install Molden in a MACOS Bigsurf. The steps that I followed: Install the compilers, gfortran,libraries, etc. extract the source from molden page. open the molden5.8 directory and from ...
Cristian Bahena's user avatar
4 votes
1 answer
233 views

Gaussian16 Raman calculation from IR checkpoint file

I already did an IR frequency calculation for my molecule. Is there any possibility to just run a Raman frequency calculation with the chk file from my IR ...
Andrea's user avatar
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