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

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1answer
34 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 ...
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1answer
34 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?
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1answer
16 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 ...
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0answers
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Input of ions and compounds in Wolfram's Mathematica [migrated]

I want to use Wolfram's Mathematica to see some data about certain ions. I don't know how to write the chemical's compounds or ions full names, so that at this time I need to write its "formula". ...
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0answers
21 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 ...
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1answer
42 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 ...
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2answers
781 views

Proper typography of “NOx”

I am a journal typesetter, and recently I came to a problem that I'm not sure I know to solve. The question is how to properly typeset the "NOx" abbreviation for nitrogen oxides. Which is ...
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2answers
95 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 ...
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1answer
43 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 ...
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1answer
86 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 ...
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1answer
27 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 ...
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2answers
32 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.
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121 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: ...
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2answers
135 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 ...
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1answer
56 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?
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2answers
196 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 ...
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4answers
426 views

How Quantum Software Packages Work?

If one wants to calculate a moderate size Alkane ( with say 10-15 Carbons , assuming 100 electrons , with Restricted Hartree Fock based methods ) we can simply say that electron-electron part will be ...
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2answers
52 views

Represent bonds spanning a unit cell boundary plane

Is there a chemical input format that is- Supported by Open Babel (and hence supports visualization in avogadro??) Can represent a bond connecting an atom to its partner in a neighbouring unit cell, ...
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3answers
90 views

Any FREE chemistry software to view molecule pictures in explorer

I am testing my small api library that generates lots of chemical files such as MOL and SDF. I was wondering if there is a software that can show me the pictures of chemical structures inside each ...
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3answers
650 views

How do I take chemistry notes on Mac?

I am learning Chemistry now, and I want to take some notes that involve huge amount of organic chemistry on Mac. How can I do that? Pages does not seem support scientific use.
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3answers
136 views

Bond angles in PDB

people I've been trying to adjust the bond angles in a protein data bank (PDB) file, but I'm a novice when it comes to computing so I would like to ask your assistance. I have a file for metamizole, ...
2
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2answers
140 views

Chemistry Spreadsheet Software?

Are there any chemistry spreadsheet-like software that: Generates 2D structure for the entered compounds (based on name or SMILES) Easy to search and create customized reports (such as similarity ...
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1answer
142 views

Halogen bonds in QuteMol

I've been using QuteMol for generating 3D animated molecular images and I've encountered a problem; for some reason that's a complete mystery to me when I create a pdb file for etravirine (using ...
4
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1answer
114 views

Learning Chemistry With Software?

I'm interested in learning organic chemistry, and am following a text (Organic Chemistry by Clayden) and an online course. I also have access to ChemBio3D. I feel as though the way chemistry is ...
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1answer
170 views

How do I overlay spectra in an ACD/NMR Processor, version 12.01?

I am having great difficulty getting spectra to overlay (the option doesn't even appear) after setting to new window mode and selecting each spectrum.
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1answer
715 views

Software for predicting chemical reactions

I wondered if it was possible to predict the product(s) of a reaction (or even the equilibrium) based on the reactants and the temperature/pressure. I found an answer to a similar question here: ...
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2answers
591 views

Program that simulates basic reactions in organic chemistry

To explain - a friend and I have been working on a program that would allow you to draw organic molecules, indicate the conditions, and predict the products. This would be primarily aimed at basic, ...
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1answer
221 views

Tools to draw molecular structure (wireframe) along with atom numbering

I am looking for open-source tools which can generate 2d molecular structure from the MOL or SMILES file. Further, it SHOULD number the atoms in the order of occurrence of atoms in the connection ...
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0answers
39 views

How can I get ChemSketch to get N and H atoms closer while still operating in ACS style and without adjusting atom sizes?

A person at wikipedia is getting on my case for creating this image because the N and H symbols are so separated even though this seems to be the default of ChemSketch (one of the softwares that's ...
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1answer
261 views

How do I get MarvinSketch to use the ACS style of drawing?

I have a Wikipedia account and the people there have a tendency for getting upset over chemical structures that I created using MarvinSketch not conforming to the ACS drawing style. Is there any way ...
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1answer
164 views

Montecarlo simulation in chemistry

I am trying to learn simulation myself and i have installed matlab in my machine for that purpose. In web i have gone through some of the basics of montecarlo simulation but i am unable to find a ...
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1answer
217 views

How would I write an input Lammps command for continuous change in temperature?

I'm going to study the thermal expansion of graphite. For this goal, I should change the temperature continuously. But I do not know how to code it by Lammps?
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3answers
204 views

Avogadro - How can bonds be hidden and only show atoms?

I am using Avogadro for visualizing some cluster systems. Is there a way to hide the bonds of the system, ie. only showing atoms? Thanks!
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3answers
395 views

Open Source tools to draw a set of 2d molecular graphs from sdf file

I have a sdf file for around 50 small-molecules for which I am doing structure-activity study. I would like to draw 2d graphs of all the molecules such that the image would fit into a single journal ...
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2answers
86 views

Mol file of Morphine

I am using the Morphine mol file and I'm attempting to create a matrix which contains a table of the atoms and how they bond similar to a ball and stick format. In the mol file bond block listed ...
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1answer
62 views

Are there computer searches for new theoretical minerals in a similar vein to Folding@Home or SETI@Home?

As a surprise gift to a friend I would like to discover a new theoretical mineral and have it named after them. I have some understanding that not all minerals have been discovered, and some minerals ...
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1answer
482 views

Tool that generates electrostatic maps of molecules?

Do you know any tools that generate electrostatic potential 2d maps of the molecules as an image?
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43 views

What's an Effective Software For Writing Out Synthesis Steps? [duplicate]

What's an effective Software For Writing Out Synthesis Steps that Works on Linux?
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1answer
113 views

Software/server for calculation of protonation states of small molecules depending on pH

For docking calculations at different values of pH, I am working with flavonoids and would like to know about any software/server that can prepare ligands depending on the pH. Up to now I read about ...
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0answers
410 views

Prediction of solubility (from chemical structure) at different pHs

I would like to know What is the best method for predicting the water solubility (and in other solvents) of a compound given its molecular structure at different pHs. What I know now is based on the ...
2
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1answer
226 views

Which Chemical Database Software Are Available?

By chemical database software I mean software with similar functionalities to Instant JChem in that they have a large database of different compounds and have the basic capabilities you, or at least I ...
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1answer
255 views

Chemical software for solving reactions [closed]

I'm looking for a software which can solve chemical equations. For example something like this (given with result): \begin{align} \ce{CH4 + 2O2 & → CO2 + 2H2O} \\ \ce{C3H6 + HCl & → ...
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4answers
38k views

How do I type a simple chemical equation in Microsoft Word?

How do I type a simple chemical equation in Microsoft Word? I can do subscripts, but long arrows are harder - they do not align with the text. Also, if I want to show a delta above the arrow for heat, ...
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1answer
1k views

Software for chemical reaction simulation [closed]

I wonder, what software packs / environments are available for chemical reaction simulation. The goal is to learn or just rehearse some basic knowledge in chemistry. I suppose there should be some to ...
6
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1answer
118 views

What does the ZZE tag in an Chemical Table file refer to?

I have a number of Chemical Table files which include a "M ZZE" tag in the properties block. For example, in Galactobuxin, I have: M ZZE 1 31 23 In ...
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156 views

How can I update a map/mesh and coordinates in a PyMol session file?

I have a PyMol session file I was using to create my figures. It contains a protein and ligand broken into several groups of atoms with a fair bit of overlap. There are also a few meshes built from ...
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3answers
4k views

What open-source software can produce 3D PDF representation of molecules?

Most of the existing software I know (like VMD or Pymol) say that they can be used to create PDF files with 3D representations of molecules: actual 3D models, which you can rotate inside the Adobe ...
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1answer
744 views

What software is used to generate the PDB molecule of the month images?

What software does the PDB use to generate these "cel-shaded" protein models with outlines around foreground atoms? (Leptin: May 2012 Molecule of the Month by David Goodsell)
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3answers
135 views

How can I perform structure alignment on an inorganic species?

I'm attempting to perform atomistic optimal structure alignment on an inorganic species. Can anyone point me in the right direction to software or a technique for performing this? There exists a wide ...
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1answer
171 views

Is the Springborg 6D phase space model used in modern molecular orbital modeling?

In a series of papers in the early 1980s, Michael Springborg explored an interpretation of the Wigner phase space function as an electron density in a six-dimensional $(q,p)$ phase space. He applied ...