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

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3
votes
1answer
177 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 ...
1
vote
1answer
32 views

How to label atoms or groups “backwards” in ChemDraw

I'm trying to draw L-tyrosine with the hydroxyl part of the phenol as HO instead of OH as it appears in the ChemDraw image. ...
2
votes
1answer
66 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 ...
2
votes
0answers
57 views

Is it possible to “brute-force” material creation through algorithms?

I know its a bit of a soft question, but lately I've wondered what important properties and calculations would a program that iterates through certain types of molecules and atoms need in order to ...
1
vote
1answer
41 views

GCMS Peak Identification: Online or Open Source / Free Programs?

Suppose I have a GCMS peak graph for a component, what are possible options to figure out what the molecule may be? Any tips about good software that will do this? I do know that for many compounds ...
0
votes
0answers
42 views

Website/software guide in synthesis of organic molecules

Does any one knows any good website/software that helps in synthesizes of low molecular wight ligands. (I mean helps you in synthesis pathway design , optimization of pathways or even just give you ...
1
vote
0answers
56 views

Warning during geometry optimization via Gaussian

I have some recurrent problem with my DFT calculations [functional: hseh1pbe; basis:6-31+g(d,p), object: porphyrin derivative]. During the MO setting I get: **** Warning!!: The largest alpha MO ...
0
votes
1answer
94 views

Titration curve graph, finding exact point of the equivalence point

I plotted all my data points and made this graph in excel. Now I need to find the volume of titrant required to read the equivalence point, as well as the pH after 18.5 mL of titrant have been ...
0
votes
0answers
12 views

how to extract data from a HPLC

The software we have is ezchrom elite, I would like to know how I can extract the profiles from this software for each sample completely ?
1
vote
2answers
55 views

Software for creating the QSAR model?

There is the .csv file with a large amount of descriptors and known experimental activity. Which software can find and describe model for prediction. Most important - numerical representation of ...
1
vote
0answers
71 views

Programs for chemical structure visualisation and drawing 2d and 3d [duplicate]

I want to create list of simple and useful software to draw molecules 2d and 3d with small description. Not necessary only freeware software. Also web-based services are interesting. Your help in ...
3
votes
0answers
58 views

Wavefunction convergence error and keywords. (Spartan)

I am currently working with Spartan software and am calculating MOs. My problem is that when I try to do calculations SCF error occures. And every time I try to put some keywords (like CONVERGE, ...
3
votes
2answers
115 views

Software for compound database creation\enumeration

The only program I have found is Plexus Suite from chemaxon. (I asked for trial, but no answer to me yet). The task is: create variation of compounds, where is scaffold and different substituents: ...
1
vote
1answer
84 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 ...
2
votes
1answer
102 views

How to optimize the molecular geometry under PyMol?

I already now about the Optimize.py plugin, which seems to be working well, but I don't see an option to prevent it from changing double bonds to single ones. If Optimize isn't capable of such, how ...
11
votes
0answers
111 views

Equivalent of Szabo and Ostlund book for DFT

Szabo and Ostlund book Modern quantum chemistry [1] is extremely useful to understand Hartree-Fock and post-Hartree-Fock methods. Not only it explains the theory behind such methods, but it is also ...
6
votes
0answers
88 views

Creating energy profile diagrams for publication

Is there automated software to create energy profile diagrams like the ones below? One could use something like Illustrator or Inkscape, but they aren't automated, are expensive (Illustrator), are ...
0
votes
1answer
40 views

Visualizing PDB file in VMD, how to upload molecules?

Problem: When I load PDB-file of my protein of interest in VMD, nothing happens. The molecules is uploaded, but when I push "D" the screens with with big "VMD" letter freezes instead of presenting the ...
5
votes
1answer
66 views

How to save the force on a molecule in GROMACS?

I am a new student of molecular dynamics. I have started using GROMACS since one month. I have a small box of 8192 molecules each with 3 atoms. I have frozen the last molecule and run the simulation. ...
0
votes
1answer
32 views

modeling structure of crystals

I came accross this image of crystal strucure in an article The Structure of Ferrihydrite, a Nanocrystalline Material by Michel et al. Does someone know the software in which it was produced. I have ...
0
votes
2answers
61 views

Is there any software to simulate a laboratory?

I wanted to do some experiments with some chemicals but unfortunately I do not have access to them. Is there any softwre I can use to get the products? I dont want to do very complicated things, I ...
0
votes
0answers
15 views

Two substrate kinetics and non-linear regression

In the case of two-substrate kinetics, it is possible to determine true Vmax an true Km via Michaelis-Menten curves, as folows: 1. : initial velocity (v0) versus [A] at fixed [B]. : Apparent Vmax at ...
5
votes
1answer
93 views

Custom-defined functionals in Gaussian 09

As stated before I want to try out custom-defined functionals. Besides the question about B3LYP itself, there is another related question. Short excerpt: $$\text{XC-Functional}=a ...
1
vote
0answers
14 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 ...
7
votes
0answers
133 views

Definition of the B3LYP functional in common QC programs

I wanted to use custom functionals with Gaussian and came up with some interesting definitions of the B3LYP functional within Gaussian, Orca and Turbomole, ... $$\small\begin{array}{lcccccc} \hline ...
2
votes
0answers
47 views

Rendering and visualization of orbitals of an atom? [duplicate]

I am looking for program that would display and render the orbitals of an atom. Preferably display all orbitals. Specifically Argon. Its not duplicate. I am looking for visual appealing rendered ...
2
votes
1answer
35 views

Do you know a simple fast front-end MD software for OS X

I need a GUI front-end simple MD software for OS X, something similar to ascalaph maybe. What I need to do is a rigid optimization of waters around a protein. I don't have many water molecules ...
0
votes
1answer
37 views

Is it possible to disable the splash screen of ChemDraw?

Is it possible to disable the splash screen of ChemDraw? I can't find a corresponding setting in the preferences dialog. Is there maybe a hidden setting / some configuration file that can be modified? ...
4
votes
1answer
795 views

Definition of Electronic energy

Using Born-Oppenheimer approximation, we separate the nuclear and electronic parts of the wavefunction, and treat them separately. We include the terms that have direct dependence on the electronic ...
4
votes
2answers
324 views

Converting a PDB file to XYZ file

I am trying to convert a pdb file of gold nanoparticle to the xyz file format to get the atomic coordinates. But when I try to use openbabel to do this, I get the following error. ...
5
votes
6answers
535 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 ...
1
vote
0answers
34 views

Is there a generic graphical language to represent chemical reactions?

I want to show a schematic representation of chemical reactions from start to finish, that will include more detailed preparation instructions than a plain chemical formula: volumes, concentrations, ...
2
votes
0answers
61 views

Program to covert WFN-file to Molden

I have tried google but without success so here the question: does anybody know a tool that can covert WFN-file to Molden or to Molpro format (including orbital info not the coordinates only).
9
votes
1answer
175 views

Trying to understand SMILES(?) patterns

In the example calculation from the conformer search package fafoom is a mysterious pattern that I'd like to understand. The SMILES code of the given example structure is: ...
6
votes
1answer
307 views

How to define a new solvent in Gaussian09 to run SCRF?

I want to run computation of my system in sulphuric acid with Gaussian 09; however sulphuric acid is not among the built-in solvents in G09. I know I have to give some parameters for the new solvent I ...
2
votes
1answer
223 views

Is there open source software for SEM EDX data analysis?

This can't be unique to me and would apply to anybody who has to use equipment in other departments has had departments move etc. What open source packages exist to read and potentially manipulate ...
1
vote
1answer
42 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 ...
17
votes
4answers
1k views

Generating neat orbitals/surfaces from molden/wfn-files

I usually use Gaussian/GaussView and don't have to bother with other programs as I think that GaussView is capable of producing nice orbital/surface pictures like this one of one of uracil's ...
3
votes
2answers
85 views

Converting mol files to InChiKey in large batches

I want to convert mol files to InChiKey. I am using OpenBabel for the conversion but I have ...
7
votes
3answers
411 views

InChIKey generation from InChI

I am trying to find some good resources to understand generation of InChIKeys from the InChI. There seems to be no resource available online. I have gone through the Wikipedia article for InChI, but ...
4
votes
2answers
120 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?
1
vote
1answer
42 views

Hide hydrogens in Molden?

I am visualizing some molecules with Molden. Is there a way to hide hydrogens, without deleting the hydrogen entries from the structure file?
3
votes
2answers
73 views

How to compute the NMR shift in Gaussian09 for only one specific atom in a bigger unit cell?

I am trying to compute the NMR shift for a specific atom in the middle of the surrounding crystal unit cell (1 surrounding anion sphere and 1 cation sphere) in Gaussian09. I only need the chemical ...
8
votes
2answers
147 views

Reliable automatic addition of hydrogens and charge assignment to small molecules at given pH?

I have some PDB structures of small molecules with missing hydrogens. Is there a software available that places missing hydrogens and assigns a charge to the molecule that is reliable? I am looking ...
3
votes
1answer
28 views

Can I disable “Display visual cues” by default in Avogadro?

These huge arrows are very annoying to me. I disable them every time I open Avogadro. Is there a way to disable them permanently?
3
votes
1answer
145 views

How can I change the bond type (single, double) of an existing bond in Avogadro?

I have a molecule extracted from the PDB. When I load it into Avogadro, it has some misplaced bond types. I want to correct this, by setting the bond type (single, double) for these bonds. How can I ...
3
votes
2answers
453 views

Naming double bond sidechain [duplicate]

In IUPAC naming double bonds take preference over an alkane chain of any length, right? So the above should be named as 2-ethylnon-1-ene. However, when I verify ...
5
votes
1answer
128 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 ...
6
votes
1answer
291 views

What is the exact meaning of GAMESS (US) SCF density convergence criteria?

In Gaussian the SCF convergence criteria is set to $10^{-N}$ by SCF=(Conver=N) Note that this criteria applies to the root mean square change in density matrix ...
4
votes
2answers
101 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 ...