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

learn more… | top users | synonyms

0
votes
1answer
37 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
19 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
27 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.
0
votes
0answers
85 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: ...
1
vote
2answers
82 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
45 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?
5
votes
2answers
104 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 ...
15
votes
4answers
372 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 ...
2
votes
2answers
41 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, ...
1
vote
3answers
81 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 ...
4
votes
3answers
492 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.
0
votes
3answers
117 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
votes
2answers
119 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 ...
6
votes
1answer
108 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
votes
1answer
104 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 ...
1
vote
1answer
117 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.
2
votes
1answer
339 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: ...
4
votes
2answers
326 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, ...
1
vote
1answer
186 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 ...
1
vote
0answers
35 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 ...
2
votes
1answer
226 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 ...
1
vote
1answer
151 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 ...
1
vote
1answer
174 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?
2
votes
3answers
168 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!
1
vote
3answers
332 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 ...
0
votes
2answers
83 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 ...
3
votes
1answer
58 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 ...
4
votes
1answer
386 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?
0
votes
0answers
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?
0
votes
1answer
108 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 ...
2
votes
0answers
357 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
votes
1answer
184 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 ...
1
vote
1answer
225 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 & → ...
10
votes
4answers
29k 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, ...
0
votes
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
votes
1answer
110 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 ...
10
votes
0answers
127 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 ...
12
votes
3answers
3k 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 ...
17
votes
1answer
654 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)
6
votes
3answers
125 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 ...
7
votes
1answer
150 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 ...
2
votes
2answers
221 views

A Chemdrawing software? [closed]

I would like to know about a Chemdrawing sotware for 2-d molecular structures. it should be mainly linux based (but if it supports other OS's then that would be great)
14
votes
3answers
807 views

What software can calculate aqueous solution equilibria?

What software is available out there to calculate the equilibrium in a set of reactions in aqueous solution? In particular, I'm interested in software general enough to simulate things like titration ...