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

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6
votes
1answer
29 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
25 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
26 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 ...
10
votes
3answers
142 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
50 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 ...
5
votes
3answers
195 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 ...
3
votes
1answer
33 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
0answers
23 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
36 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 ...
7
votes
2answers
89 views

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

I have some molecular PDB structures with missing hydrogens. Is there a software available that places missing hydrogens and assigns a charge to the molecule that is reliable? I have used Avogadro to ...
3
votes
1answer
24 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
47 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
53 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
71 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 ...
5
votes
1answer
135 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
90 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 ...
5
votes
1answer
219 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
votes
2answers
159 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 ...
5
votes
5answers
256 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 ...
5
votes
1answer
51 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
votes
1answer
36 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
votes
1answer
97 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 ...
3
votes
1answer
87 views
0
votes
1answer
66 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
votes
0answers
23 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
votes
1answer
77 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
votes
1answer
52 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 ...
3
votes
1answer
59 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 ...
3
votes
1answer
57 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 ...
5
votes
1answer
57 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 ...
3
votes
2answers
78 views

Calculating reaction products programmatically?

I was wondering if there was a known algorithm which could calculate simple reaction products - not anything organic, but things like $$\ce{NaBr + LiF -> NaF + LiBr}$$ While these are quite ...
6
votes
1answer
78 views

Software for viewing a structure and altering bond angles

Does anyone know of any good software that would allow me to view the structure of a compound while also allowing me to change the bond angles in the structure (and give me numeric values for those ...
-2
votes
1answer
73 views

installation error of dalton 2015 in ubuntu 12 [closed]

what are the answer for CONFIRMATION OF REGISTRATION when register in dalton forum ? install got error, how to install dalton 2015 wonder@wonder-VirtualBox:~/dalton/DALTON-Source$ uname -r ...
5
votes
1answer
61 views

Viewing a protein or bio structure in Chembio3D in its natural conformation

I notice when using SMILES or a IUPAC name for many molecules and generating them in Chembio3D, and then running MM2 > Minimize Energy, the structures produced are most of the time not reflections of ...
3
votes
2answers
80 views

Gaussian Convergence Issue for N2+N PES

I am trying to obtain a potential energy surface (PES) for $\ce{N2 + N}$ combination using scan feature of Gaussian. I have tried different combinations of basis ...
2
votes
1answer
53 views

CASTEP Geometry Optimization Movie

I am using a calculation software called CASTEP, within Materials Studio, and I want to make a "movie" of my geometry optimization, but don't know how to. CASTEP allows one to do many many different ...
3
votes
0answers
50 views

Cis/Trans-Decalin in ChemBio3D

According to my organic chemistry textbook, Cis-Decalin has the two rings nearly perpendicular to one another, with the middle hydrogens cis to one another. Trans-Decalin has the ring nearly flat ...
0
votes
0answers
22 views

Free software to change XRD stepsize

I have some data with a non-integer stepsize and I want to manipulate it to have an integer stepsize. I have done this many times in the past using MDI Jade, but this is commercial software and I no ...
2
votes
1answer
78 views

How to run crystal simulation on GAMESS?

I know GAMESS is not best suited for crystal simulation but I am not ready to start learning another package as VASP. As I heard GAMESS is able to do some calculations in a "terminated" crystal (I ...
1
vote
1answer
57 views

Consistent atom names PDB

Lets say you have two times the same molecule in PDB format. PDB1: ...
3
votes
1answer
123 views

Why is predicting products of chemical reactions difficult? [closed]

I was going to ask whether there are software that could be used to predict the products of any given chemical reaction. However, I then noticed these two earlier questions Chemical software for ...
1
vote
1answer
58 views

Comparing adamantane carbon types for accepting OH using MM ForceField

I want to compare two type of carbons accepting OH in adamantane which I've shown below. I know the blue position is preferred. But I wanna prove it with energy optimization and MM Forcefield. I ...
2
votes
1answer
52 views

How do I convert zwitterions to neutral form in Avogadro?

I'd like to be able to convert zwitterions to neutral form in Avogadro if possible. How do I do this?
0
votes
1answer
55 views

What does C-OXT stand for in PDB files?

I've been trying to create 3D structures of unionized tyrosine (and other amino acids, it's just tyrosine is the one I'm up to atm) using the structure of Zwitterions found within PDB files and to do ...
2
votes
1answer
142 views

How does one export a PDB structure to SVG?

This question is one that I'm wondering whether it belongs here or on Graphic Design SE. All I want is some software that can export a PDB structure of a protein (displayed in ribbons style) or DNA ...
1
vote
1answer
57 views

How do I make PDB 1HIG's data usable for producing ball-and-stick models?

PDB: 1HIG, when opened using Accelrys DS Visualizer, Avogadro and Jmol produces a series of dots in space and cannot be displayed as 3D ball and stick models. Is there any way to overcome this ...
3
votes
2answers
197 views

Is there any free GAMESS input file maker for Mac OS?

My main purpose is to simulate excited state calculations on a molecule with Time Dependent DFT. I am looking for free software that makes input files for GAMESS. I have tried Avogadro and it works ...
1
vote
1answer
47 views

Finding compounds with B, Si, Ca, and Mg in differing amounts

Not sure if my question is better suited to a software related group, but here goes: Is there a software program that lets you add differing amounts of elements, minerals, etc., then tells you what ...
0
votes
1answer
343 views

How do I write a valid CIF, PDB or XYZ file from the coordinates listed below?

I want to create a 3D molecular file using coordinates taken from: Hrynchuk, RJ; Barton, RJ; Robertson, BE (1983). "The crystal structure of free base cocaine, C17H21NO4" (PDF). Canadian Journal of ...
0
votes
1answer
55 views

Where can I find a complete and accurate table of CPK colours?

I have been using several chemical drawing softwares including MarvinSketch, Jmol, Accelrys DS Visualizer, Avogadro, etc., all of which I have set to CPK colouring. Despite this supposedly common ...