Re: [Avogadro-Discuss] [Avogadro-devel] Workflow Scripts (for Avo2)

On Wed, Dec 28, 2016 at 3:04 PM, Gary Kedziora wrote: > Have you looked at pymatgen? It has a lot of useful features for crystal > structures and some also for molecules as well. > > I have been looking at pymatgen, but hadn't thought about it in this context. We should

Re: [Avogadro-Discuss] paid modeling work and/or tutor

On Thu, Nov 10, 2016 at 12:34 PM, Tim Potter wrote: > Thank you so much for your offer to help. I'm happy to help user document > avogadro when you get to that point. I started trying avogadro 2 because > avogadro 1 was not saving double bonds, and was also not aware

Re: [Avogadro-Discuss] paid modeling work and/or tutor

On Tue, Nov 8, 2016 at 12:44 PM, Tim Potter wrote: > Hello > > I'm very slowly working through making avogadro2 functional to calculate > electron density, bond strain, and total energy for a new carbon molecule. Avogadro 1 and 2 provide a method of generating input for

Re: [Avogadro-Discuss] AutoOptimization

It would be good to do some verification on this, because in my testing this was consistently the location of the executable. We could add some code to print out what it sees, or try to reproduce this locally. There is quite a bit of work in several projects I work on where we successfully rely

Re: [Avogadro-Discuss] Issue building from source (undefined reference to symbol 'XInitThreads')

On Tue, Mar 29, 2016 at 1:58 PM, Miro Moman wrote: > Hello, > > I am struggling to build Avogadro 1.1.1 from source in Ubuntu 15.10 x86-64. > > I run > > cmake ../ > -DEIGEN2_INCLUDE_DIR=/home/administrator/Downloads/avogadro/eigen-eigen-b23437e61a0 > > followed by make > >

Re: [Avogadro-Discuss] importing molecule by name

On Thu, Nov 19, 2015 at 10:35 AM, Steven Wathen wrote: > Hello, > > For some reason the Import - Fetch by chemical name function in Avogadro is > not working today. When I try I get en error message: Specified molecule > could not be loaded: toluene.sdf > > I takes a

Re: [Avogadro-Discuss] [Avogadro-devel] New Avogadro Manual

On Mon, Aug 31, 2015 at 4:51 PM, Geoffrey Hutchison wrote: > Thanks to support from the University of Pittsburgh Department of Chemistry, > there is a new manual for Avogadro: > http://ghutchis.gitbooks.io/avogadro/ > > You can find the images and Markdown on GitHub,

Re: [Avogadro-Discuss] orbital visualisation with Gaussian formatted checkpoint files

On Sat, Jun 20, 2015 at 10:38 AM, Jose A Gamez joseantonio.ga...@uam.es wrote: Hi everybody, I have a organometallic complex whose wave function I’ve calculated with G09 (UDFT, as it’s a quintet, TPSSh/def2-SVP). I open Gaussian's formatted checkpoint with Avogadro to draw the orbitals.

Re: [Avogadro-Discuss] docking small molecule againt a small molecule

Hi, On Thu, Apr 9, 2015 at 9:36 AM, mirko busato mirko.bus...@gmail.com wrote: Dear all, Is there a way with Avogadro to perform a small molecule/small molecule docking? I see papers citing Avogadro that do docking, but I think they often use it for the small molecule piece. This is

Re: [Avogadro-Discuss] Windows / Ubuntu Avogadro Differences

Hi Darren, On Thu, Apr 16, 2015 at 4:43 AM, darren.rhodes darren.rho...@gmail.com wrote: Hi All I have Avogadro at home (Ubuntu) and at work (Windows). They are both the same version but the Windows Avogadro allows for conformer searching (Extensions/Molecular Mechanics/Conformer Search)

Re: [Avogadro-Discuss] avogadro crashes X on ubuntu 14 under vnc

Hi Ron, What VNC server/client are you trying to use? I have Ubuntu 14.04 and could try to replicate, I would expect this to work with VNC, the major complication is often getting a good OpenGL context but VNC usually does rendering on the server-side and simplifies this. Thanks, Marcus On

Re: [Avogadro-Discuss] New CP2K input generator in Avogadro,

On Mon, Mar 23, 2015 at 6:14 PM, Željko M. Svedružić zsved...@biol.pmf.hr wrote: For those of you who like to work with CP2K, we are happy to tell you that we have prepared an input generator in Avogadro http://cp2k.org/tools This looks great, I will try to get it tested and make sure we

Re: [Avogadro-Discuss] Avagadro-lammps

On Tue, Jun 24, 2014 at 8:31 PM, S Arun Srikant Sridhar ss3...@drexel.edu wrote: Can some body please tell me whether avagadro can create lammps input data file It cannot at this time - I have been looking into LAMMPS, and how we might produce input for MD codes in general but we don't have

Re: [Avogadro-Discuss] How do I access the Z-matrix tool?

Hi Rick, On Mon, Apr 7, 2014 at 12:46 PM, Rick Muller rpmul...@gmail.com wrote: I'm interested in using the Z-matrix tool in Avogadro. I'm currently using Avogadro v1.1.1, and the tool does not appear in the toolbar or the menus. Can I enable it, or do I need to download a newer build to get

Re: [Avogadro-Discuss] How do I access the Z-matrix tool?

to help with the former, but probably not the latter. Rick On Mon, Apr 7, 2014 at 10:51 AM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: Hi Rick, On Mon, Apr 7, 2014 at 12:46 PM, Rick Muller rpmul...@gmail.com wrote: I'm interested in using the Z-matrix tool in Avogadro. I'm

Re: [Avogadro-Discuss] Python terminal

On Thu, Apr 3, 2014 at 2:23 PM, G M jakm...@yahoo.it wrote: Hi all, I would like to use python terminal, I followed the tutorial in the documentation page but there is no Python terminal option in my Avogadro 1.1.0 or 1.1.1. I'm in a MacOX mountain lion, I've tried to begin a discussion in

Re: [Avogadro-Discuss] can I get removed form this list?

If you follow the link below (included in every email to the list) you can unsubscribe there. https://lists.sourceforge.net/lists/listinfo/avogadro-discuss On Thu, Apr 3, 2014 at 2:24 PM, Andy Engelkemier andy.engelkem...@gmail.com wrote: thanks

Re: [Avogadro-Discuss] Delete some atoms in a supercell

On Tue, Oct 1, 2013 at 2:07 PM, Sara Yzdn saray...@gmail.com wrote: Hi, I have generated a supercell in avogadro. I want to remove some of the atoms. Is there a way I can remove them by the aid of the gui and not guessing their position in the Cartesian built? You can use the selection

Re: [Avogadro-Discuss] cube files

Do you know if the full data set can be downloaded, and what license they applied to the data? It looks like it could be a useful data set, but from the site I didn't see clear licensing or a data download link. We are working on a demo with Avogadro, web services, and chemical data and I am

Re: [Avogadro-Discuss] Error message in saving animations

On Sat, Jun 29, 2013 at 6:52 PM, MD MAHBUBUL ISLAM mmi...@psu.edu wrote: Hello, I am trying to make animation using Avogadro 1.1.0 version. When I intend to 'save as .avi' it gives an error message of 'could not run povray'. I installed povray in my laptop, but I don't understand- how I can

Re: [Avogadro-Discuss] read gaussian input file?

Hi, On Sun, May 12, 2013 at 9:55 AM, Randy Bin Lin mumuwe...@gmail.com wrote: hi all I noticed that avogadro is able to read in gaussian output file. can it read in its input file or is there a plan to do that? it will be very helpful with preparing a gaussian job. I have never liked the

Re: [Avogadro-Discuss] segfault or reading ABINIT file

On Mon, Apr 29, 2013 at 2:12 PM, Cohen, Ron rco...@carnegiescience.edu wrote: The reproducible error is: snip Program received signal SIGSEGV, Segmentation fault. [Switching to Thread 0x40602940 (LWP 17304)] OpenBabel::ABINITFormat::ReadMolecule (this=optimized out, pOb=optimized out,

[Avogadro-Discuss] First Avogadro 2 beta release

Hi, I wanted to let people on these lists know that we just made our first beta release of Avogadro 2, along with MoleQueue and MongoChem. Please see the blog post here, http://blog.cryos.org/archives/265-First-Open-Chemistry-Beta-Release.html We have created binary installers for Windows and

Re: [Avogadro-Discuss] Avogadro to lammps

On Wed, Mar 6, 2013 at 3:02 PM, Ibrahim (Ibrahim Awad) Awad iea...@crimson.ua.edu wrote: I've built my structure on avogadro and i want to create lammps data file that contains atoms, bonds and angles. How can i do that please LAMMPS is something David Lonie worked on recently in Avogadro 2,

Re: [Avogadro-Discuss] Problem loading files through a python extension

Hi, On Thu, Mar 7, 2013 at 3:20 PM, Mason, Nicholas nicholas.maso...@imperial.ac.uk wrote: Hello, I have been writing a python extension to add ORCA support to Avogadro. The extension so far consists of a input generator, which works nicely, and an output-file reader, which I can't seem to

Re: [Avogadro-Discuss] installation problems

On Wed, Mar 6, 2013 at 6:06 PM, Cohen, Ron rco...@carnegiescience.edu wrote: I built avogadro but get a segfault when I try to run. Is the problem that it is not finding the translations? Any suggestions? Thanks, Could you run this from gdb and post the backtrace? I haven't seen this, and there

Re: [Avogadro-Discuss] installation problems

On Tue, Mar 12, 2013 at 2:19 PM, Cohen, Ron rco...@carnegiescience.edu wrote: I finally got it to run. The problem was in my openbabel installation, as I found by gdb. The problem was multiple versions of libraries and or trying to use the intel compilers. I switched to gnu and made sure

Re: [Avogadro-Discuss] Where to click on a hydrogen

On Tue, Mar 5, 2013 at 4:24 AM, Noel O'Boyle baoille...@gmail.com wrote: Hey there, I used an automated GUI tester to investigate where Avogadro accepts clicks on a hydrogen: http://baoilleach.blogspot.co.uk/2013/03/avogadro-hydrogen-clicking-craziness.html (see comments there also for a

Re: [Avogadro-Discuss] cut-n-paste in Avogadro running on Ubuntu

Hi, On Sat, Jan 19, 2013 at 10:52 AM, fredrik haeffner jfhaeff...@hotmail.com wrote: Hi! Avogadro's cut-n-paste doesn't work for me running on Ubuntu. Yes, you can copy a XYZ-file from a terminal window and paste it into Avogadro. However, say, you select 3 atoms in Avogadro and copy-n-paste

Re: [Avogadro-Discuss] Inability to calculate carbon dioxide dipole moment?

On Sat, Jan 19, 2013 at 12:31 PM, Steven Petrovic petro...@sou.edu wrote: Hello, Despite how wonderful I think Avogadro is for molecular modeling and its potential for educational purposes, I hesitate to use Avogadro in the chemistry laboratory when there seems to be such glaring issues as

Re: [Avogadro-Discuss] cut-n-paste in Avogadro running on Ubuntu

On Sat, Jan 19, 2013 at 1:23 PM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: Hi, On Sat, Jan 19, 2013 at 10:52 AM, fredrik haeffner jfhaeff...@hotmail.com wrote: Hi! Avogadro's cut-n-paste doesn't work for me running on Ubuntu. Yes, you can copy a XYZ-file from a terminal window

Re: [Avogadro-Discuss] Configure Avogadro on Cent OS

On Sat, Sep 15, 2012 at 5:21 PM, Ismail, Mohd F. fa...@ou.edu wrote: As a solution, I managed to compile Avogadro using avogadro-squared, as mentioned on Avogadro this (http://avogadro.openmolecules.net/wiki/Compiling_on_Linux_and_Mac_OS_X) Avogadro wiki page. Hopefully it'll help saves some