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Questions tagged [software]

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

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6 votes
1 answer
88 views

Achieving Consistent Molecule Size in ChemDraw for Publication

I'm currently preparing an article and need to ensure all molecules depicted with ChemDraw are consistently sized when pasted into my document. I've encountered an issue where the sizes vary ...
0 votes
0 answers
16 views

Seeking Comprehensive GHS Hazard Database for Chemicals

I have been using PubChem as a source for GHS hazard information, but I have noticed that the database is incomplete for some chemicals. While PubChem is a great resource, I am looking for a more ...
1 vote
0 answers
8 views

Adding a molecule in AMBER [migrated]

I'm new to computational chemistry. I want to model the enzyme EGFR and a small molecule Lapatinib. I got a .pdb file of EGFR at the Alphafold website, and got a .sdf file of Lapatinib at the pdb site....
2 votes
2 answers
201 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 ...
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 ...
8 votes
1 answer
698 views

How to prevent water from abandoning solvent box during molecular dynamics simulation with AMBER?

I ran a molecular dynamics simulation for a small polypeptide and TIP3P water with AMBER using solvatebox function with with a distance of 15 Å between the molecule ...
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 ...
4 votes
1 answer
150 views

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 ...
9 votes
2 answers
394 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 ...
10 votes
1 answer
494 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 ...
0 votes
0 answers
45 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 ...
0 votes
0 answers
59 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 ...
1 vote
1 answer
659 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 ...
0 votes
0 answers
66 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 ...
1 vote
1 answer
191 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 ...
0 votes
0 answers
20 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 ...
1 vote
0 answers
68 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 ...
0 votes
0 answers
24 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. ...
1 vote
0 answers
65 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 $\ce{N2}$...
3 votes
1 answer
332 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 ...
3 votes
5 answers
2k views

How to delete everything but a specific ligand from a PDB file using Linux-compatible free software?

I would like to delete everything from a PDB file except a specific ligand that I know the PDB code for. Is there a simple way to using free Linux-compatible software? If you want a specific example ...
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?
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: ...
1 vote
1 answer
504 views

Computational chemistry software to generate files of cartesian coordinates and zmatrix of molecules

Is there any software that I can provide bond lengths, bond angles and torsion dihedrals of a molecule and generate an output file in the format of cartesian coordinates or zmatrix? Example: I would ...
15 votes
2 answers
456 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 ...
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): ...
-2 votes
1 answer
4k 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 ...
2 votes
1 answer
324 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 ...
3 votes
1 answer
337 views

Is there a Python module for calculating Ovality of a molecule?

Ovality gives a measure of how the shape of a molecule approaches a sphere (at one extreme) or a cigar shape (at the other). Ovality is described by a ratio of volume to area (see https://en.wikipedia....
4 votes
1 answer
104 views

Detect the presence of non stereochemically annotated atoms in mol files

I'm facing a problem now and I don't know where to start from. I'm treating databases in which there are mol-files that have stereo-chemical carbons, which, sometime, are not annotated as being R/S or ...
6 votes
4 answers
1k views

Software recommendations for overlaying molecular structures

I am looking for a program to overlay the structures of small molecules as an aid for my students in comparing the results of optimization geometries using different optimization methods. At this ...
1 vote
1 answer
466 views

Valency of each atom in a molecule with python

Consider ethanol, where each carbon atom has a valency of 4 and oxygen a valency of -2. I would like to determine these values for many compounds given their SMILES or InChI keys. (For the purpose of ...
4 votes
2 answers
3k 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 ...
1 vote
0 answers
160 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 (...
6 votes
3 answers
1k 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 ...
1 vote
0 answers
24 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 ...
0 votes
0 answers
107 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 ...
-3 votes
1 answer
270 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?
3 votes
1 answer
233 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/...
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 $...
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 ...
0 votes
0 answers
48 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 ...
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?
1 vote
1 answer
464 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 ...
3 votes
3 answers
2k views

An automated approach to visualize several xyz structures

I have several .xyz files (each composed of several molecules) and I'd like to find an automated way to visualize and save them. I'd appreciate any guidance.
1 vote
1 answer
148 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 ...
22 votes
1 answer
579 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 ...
4 votes
0 answers
269 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 ...
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 ...
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 ...

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