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

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1answer
69 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 ...
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0answers
51 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 ...
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0answers
44 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 ...
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1answer
34 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 ...
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1answer
38 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. ...
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1answer
30 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 ...
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2answers
51 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 ...
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0answers
12 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 ...
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1answer
64 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 ...
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0answers
13 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 ...
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0answers
104 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 ...
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0answers
45 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 ...
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1answer
30 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
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1answer
31 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
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1answer
478 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 ...
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2answers
176 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. ...
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6answers
409 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 ...
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0answers
29 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, ...
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0answers
51 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).
8
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1answer
160 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
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1answer
201 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
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1answer
137 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
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1answer
36 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 ...
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4answers
813 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 ...
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2answers
73 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 ...
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3answers
353 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
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2answers
112 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?
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1answer
38 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?
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2answers
63 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 ...
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2answers
136 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
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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
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1answer
99 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
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2answers
271 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
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1answer
119 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 ...
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1answer
250 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 ...
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2answers
99 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 ...
6
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1answer
383 views

What is GAMESS and Gaussian?

I've been seeing a lot of GAMESS and Gaussian questions around here, and most of them seem very hard to answer. I extrapolated that they might be some sort of Chemistry programs, but what do they do ...
8
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2answers
221 views

How do I create a spreadsheet containing the coordinates and predicted bond angles, molecular properties, torsion properties, etc of a molecule?

On a previous answer here (http://chemistry.stackexchange.com/a/30841/876) I was informed in the comments that OpenBabel & Python terminal could be used to print the data contained in the property ...
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5answers
397 views

How can I calculate the charge distribution of a water molecule?

I would like to obtain the 3D charge density of a water molecule for plotting purposes (i.e. not necessarily super-accurate). I know this is a tough problem, but I'd like to give it a try. Since I'm ...
7
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2answers
94 views

What program could I use to create a protein model from scratch?

I would like to create protein models such as the ones in the Protein Data Bank. I have got GROMACS but I don't know if it can be used to model macromolecules.
4
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1answer
55 views

Modified DNA bases in Pymol and Coot

When using Pymol or Coot molecular visualization software to solve x-ray crystallography structures, how can I mutate a cytosine to a 5-methylcytosine?
4
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1answer
153 views

How do I print property matrices in Avogadro?

I'd like to print the content of property matrices (i.e., the matrices shown after selecting View→Properties→X where X is one of the six options shown, including ...
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1answer
93 views
0
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1answer
75 views

Is there any required data missing from my CIF file?

I previously asked a question about a CIF file here (namely CIF fields that are available for some atoms, but not others) I think I have the answer (namely to place dots [.] at places where the two ...
0
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1answer
52 views

CIF fields that are available for some atoms, but not others

I've been working on another CIF file, this time for (-)-threo-methylphenidate based on Pharma Res, 1995 (sadly the relevant crystallography data isn't supplied in the free preview at Springer). I ...
4
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1answer
106 views

Azathioprine CIF data file rendering problem in Accelrys

I have been working on a CIF data file (URL: http://goo.gl/2cprI6) based on data from this experiment: Acharya, 1984 (free full text isn't available, but the page [page 2] with the experiment details ...
2
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1answer
83 views

How do I write many cyclic voltammetry curves in Nova?

We are making an electrochemical research on supercapacitors that involves checking stability of our material. That requires repeated writing of cyclic voltammetry curves. Our goal is to write at ...
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1answer
73 views

Software for technical calculation of chemical reactors

I'm not a chemical engineer and don't have good background in it. Just my father asked me to do something for him, as I'm a computer engineering graduate. This is a software for calculation of ...
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2answers
179 views

How to make a CP2K input file with Avogadro?

I am trying to learn to work with CP2K and now need to make its input file. CP2K has kind of adaptor for Avogadro2 but not Avogadro ( I don't know what is the relation between them !). I also tried ...
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1answer
141 views

Any free tool for Calculating Gasteiger-Hückel charges for ligands?

I want to know if there is any free open source tool available for Gasteiger-Hückel charge calculation? I know it is available on Sylbyl but is there any other(free) way to calculate these charges for ...