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

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4
votes
3answers
171 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
26 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
20 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
29 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
84 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
22 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
45 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
50 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
64 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
121 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
85 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
194 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
152 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 ...
6
votes
4answers
202 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
49 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
33 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
90 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
85 views
0
votes
1answer
61 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
70 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
41 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 ...
2
votes
1answer
30 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
50 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
50 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
77 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
69 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
63 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
59 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
74 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
43 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
20 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
64 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
52 views

Consistent atom names PDB

Lets say you have two times the same molecule in PDB format. PDB1: ...
3
votes
1answer
117 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
56 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
50 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
49 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
109 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
56 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
186 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
279 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
49 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 ...
0
votes
2answers
38 views

What is the official file extension for SMILES and SMARTS files

I want to know what is the officially used file extension for files containing SMILES and SMARTS strings. Somewhere I see .SMI/.SMA and somewhere its the full .SMILES/.SMARTS.
1
vote
0answers
215 views

How to Locate the Excited State Dipole Moment in Turbomole Output (TD-DFT)

I want to calculate the dipole moment for the first excited state with a Q.C. program (TURBOMOLE: TD-DFT). The calculation lists the following output: ground state total dipole moment: ...
2
votes
2answers
243 views

Freeware that converts structure in a conformational model?

In order to draw chemical structures I use ChemBioDraw Ultra. As an exercise I've to draw the most stable conformation. I expect a twist-boat like structure (instead of usual chair conformation ...
0
votes
1answer
67 views

Chemdoodle to mestranova

Is it possible to copy my chemdoodle displayed structure into mestranovea? I have tried simple dragging (mac) and all the various copy/paste options... any ideas?
7
votes
2answers
309 views

Methods for Determining Partial Charges

I want to run classical molecular dynamics simulations of a periodically replicated surface (rutile $\ce{TiO2}$ with grooves). In order to do so, I first need to solve for the partial charges residing ...