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

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3
votes
0answers
15 views

Charge consistency in fragment qm/mm methods

I'm calculating the multipole moments on several fragments of a molecule. What are some procedures to ensure that the charges etc are representative of the complete molecule? How do I ensure I'm not ...
5
votes
1answer
36 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
65 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 ...
3
votes
1answer
46 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 ...
-3
votes
1answer
35 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
46 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
38 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 ...
3
votes
0answers
40 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
12 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
38 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
43 views

Consistent atom names PDB

Lets say you have two times the same molecule in PDB format. PDB1: ...
4
votes
1answer
88 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
48 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
47 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
27 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
66 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
50 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 ...
16
votes
2answers
796 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 ...
2
votes
2answers
134 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
46 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
170 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
38 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
36 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
177 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
198 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
62 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?
6
votes
2answers
256 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 ...
19
votes
4answers
505 views

How do 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
68 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
100 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
805 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
153 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
165 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
164 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
124 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
250 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
1k 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: ...
5
votes
2answers
916 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
264 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 ...
2
votes
1answer
220 views

Free automatic organic synthesis Linux command line program

I'm trying to find a free automatic organic synthesis Linux command line program which take mol or smile files as input. I have random molecules and I'd like to know how difficult above a baseline ...
1
vote
0answers
46 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
308 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 ...
2
votes
1answer
178 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
241 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
256 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
454 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
93 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
92 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
609 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?
1
vote
3answers
139 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 ...