Questions tagged [software]
For questions pertaining to software used by chemists for professional or academic purposes.
375
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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 ...
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14
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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 ...
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41
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"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
...
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1
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82
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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 ...
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22
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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. ...
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47
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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 $\ce{N2}$...
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3
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1
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119
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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 ...
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227
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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 ...
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1
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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 ...
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2
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102
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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 ...
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100
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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 (...
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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 ...
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74
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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 ...
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200
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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?
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198
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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/...
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44
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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 ...
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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?
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358
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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 ...
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135
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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 ...
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193
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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 ...
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281
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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 ...
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1
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119
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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 ...
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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 ...
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Troubleshooting an Autodock Vina Error on Chimera: "Could not find an atomic number for Hn Hn"
After having minimized a ligand (that I prepared on Marvinsketch), and after having prepared a target enzyme to dock said ligand onto (collected from RCSP PDB), I was met with an error by the reply ...
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4k
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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 ...
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252
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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 ...
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176
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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 ...
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1
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58
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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 ...
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262
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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:
$...
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262
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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 (...
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797
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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. ...
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42
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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 ...
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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 ...
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6
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1
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222
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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 ...
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1k
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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 ...
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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 $\ce{COOH},$ ...
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2k
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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 ...
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842
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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 ...
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2
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766
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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 ...
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1k
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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 ...
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1
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8k
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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 ...
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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 ...
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7
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268
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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"....
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657
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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 ...
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1
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134
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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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234
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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 ...
4
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1
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212
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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 ...
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Correlating specific heat (Cp) of a substance with other substance on the basis of similar physio-chemical properties
I am modelling $\ce{H2O2}$ decomposition in ANSYS Chemkin-Pro and I have difficulty finding $C_p$ (specific heat at constant pressure) for liquid $\ce{H2O2}$ for various temperature ranges.
My ...
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Software for determining symmetry elements and point group of drawn molecules
The title represents my overall question. I would like to have a software that able to draw molecules (especially coordination complexes) and determine the symmetry elements and point group of the ...
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104
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XSteam IF97 tables (MS Excel version) lack of inputs [closed]
I am using XSteam IF97 to evaluate steam power plant cycles.
However, I miss some important input options such as pressure as a function of entropy and temperature ("p_st()") - when I assume ...
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