Re: [Avogadro-Discuss] Conformer search

On Mon, Dec 19, 2011 at 2:17 PM, Geoffrey Hutchison ge...@geoffhutchison.net wrote: Is there currently a GUI-based method to generate and view conformations of a molecule? Using the forcefield extension, I appear to be generating the conformers, but in View Properties Conformer Properties,

Re: [Avogadro-Discuss] error during conformational search

On Thu, Mar 15, 2012 at 11:52 AM, Geoffrey Hutchison ge...@geoffhutchison.net wrote: I'm a Phd student and I'll have to do 'systematic research of rotors' even for much larger molecules. You may want to investigate the genetic-algorithm and Monte Carlo weighted search options in Open Babel

Re: [Avogadro-Discuss] Binary RPM for CentOS 5.8 ... ??

On Fri, Feb 1, 2013 at 4:42 PM, Richard Walsh richard.wa...@csi.cuny.eduwrote: After a frustrating day of trying to install everything required for Avogadro 1.1.0 (Babel, Eigen, Qt, cmake, wxWidgets) on a CentOS 5.8 system (although with no issues specific to CentOS) I am wondering if there

Re: [Avogadro-Discuss] Avogadro 1.1.0 cannot deal with files with certain names?

On Fri, Feb 1, 2013 at 5:40 PM, Xing xi...@pitt.edu wrote: Dear all, The attached pdbs are two identical files from Protein Data Bank. The one with the original name 2K4G.pdb will cause Avogadro 1.1.0 to crash (see 2K4G.log) and just changing the name from 2K4G.pdb to 2K4G_avo.pdb will prevent

Re: [Avogadro-Discuss] Avogadro 1.1.0 cannot deal with files with certain names?

On Sun, Feb 3, 2013 at 10:26 AM, Xing Yin xi...@pitt.edu wrote: Wow, I do have 2K4G.aux (generated by MOPAC2012) in the same directory as 2K4G.pdb. Once I copy 2K4G.pdb into a new folder, it can be read by Avogadro 1.1.0 without a problem just like 2K4G_avo.pdb. Simply symlink 2K4G.pdb to

Re: [Avogadro-Discuss] Avogadro 1.1.0 cannot deal with files with certain names?

, Univ Pittsburgh G-3 Chevron Science Center 219 Parkman Ave Pittsburgh, PA 15260 On 02/03/2013 10:58 AM, David Lonie wrote: On Sun, Feb 3, 2013 at 10:26 AM, Xing Yin xi...@pitt.edu wrote: Wow, I do have 2K4G.aux (generated by MOPAC2012) in the same directory as 2K4G.pdb. Once I copy

Re: [Avogadro-Discuss] crash loading GAMESS log files

Hi Blake, I tried using the 1.1.0 version on the sourceforge site, and also saw the crash with this log file. I built a new version from the 1.1.0 git tag against an up-to-date openbabel, and the new version works. I've uploaded an installer here:

Re: [Avogadro-Discuss] Unit cell builder

On Wed, Feb 27, 2013 at 2:21 PM, Richard Overstreet reoverstre...@catamount.wcu.edu wrote: Hello all, I have a problem with the unit cell builder. I am able to successfully build a unit cell where a = b = c = 2 and alpha = beta = gamma = 108 with NH3BH3. However, when I go to export the

Re: [Avogadro-Discuss] rotating a bond

Hi, The easiest way is to use the bond-centric manipulation tool. See the icon for the tool and instructions on this page: http://avogadro.openmolecules.net/wiki/Bond_Centric_Manipulate_Tool Hope this helps, Dave On Sat, Mar 2, 2013 at 6:54 AM, Isidoro A. Gómez Parrales ian...@us.eswrote:

Re: [Avogadro-Discuss] building slab with avogadro

On Thu, Mar 14, 2013 at 5:51 PM, Rupashree Shyama Ray shyama@gmail.comwrote: Hi, While building input files for quantum espresso, certain atoms are duplicated in avogadro. Can anyone suggest how to deal with the problem within avogadro? It's terrible to do a trial and error to remove

Re: [Avogadro-Discuss] problem with libpng(no atom display)

On Thu, Apr 18, 2013 at 12:31 PM, Ganesh, Panchapakesan gane...@ornl.gov wrote: I believe I am having the same problem. While I could get avogadro working nicely on my mac, an ubuntu 12.04 installation either from the ubuntu-repo or compiling from source-code from

Re: [Avogadro-Discuss] Reg- compiling error Avogadro

On Tue, Apr 23, 2013 at 1:11 PM, Dr. Amar Bahadur amar.b@gmail.com wrote: Dear Users, While compiling AVOGADRO, in Fedora-17, I got following error message: [dramarbahadur@dramarbahadur build]$ cmake ../ snip -- checking for module 'openbabel-2.0=2.3.0' -- package

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

Hi Ron, Thanks for the report. Is this issue fixed by the patch you sent, or is this a separate issue? Dave On Mon, Apr 29, 2013 at 2:12 PM, Cohen, Ron rco...@carnegiescience.edu wrote: The reproducible error is: New Thread 0x40200940 (LWP 14602)] Settings are missing for the next engines:

Re: [Avogadro-Discuss] The defect site changes place after rotation!

On Tue, May 21, 2013 at 5:58 AM, 李文凡 limurphy1...@gmail.com wrote: Dear Avogadro users, I am visualizing a supercell containing two defect sites, but after rotating the cell, the defect site changes place! It is really terrifying as I can not determine the exact defect site by viewing it.

Re: [Avogadro-Discuss] The defect site changes place after rotation!

On Tue, May 21, 2013 at 8:05 AM, 李文凡 limurphy1...@gmail.com wrote: Dear Dave, Thank you for your follow-up. For rotation, I mean I drag the cell (pressing the right bottom of my mouse), so it can be rotated around certain axis. The right mouse button doesn't perform rotations, it will

Re: [Avogadro-Discuss] creating *.mol file

Hi Brent, Did you try: File Save as mymolecule.mol? Best, Dave On Wed, May 29, 2013 at 2:28 PM, Brent Friesen ochemonl...@gmail.comwrote: I would like to use Avogadro as a way to create energy-minimized molecular conformations for an NMR prediction platform called PERCH. PERCH will only

Re: [Avogadro-Discuss] About nanotube builder in Avogadro

On Thu, Aug 8, 2013 at 12:48 PM, Hyun-seok Kim roite...@snu.ac.kr wrote: Hi, I’m Hyun-seok Kim a graduate student at Seoul National University in South Korea. While using the ‘nanotube builder’ included in Avogadro I’ve noticed that (n,m) specification of nanotube is restricted maximum up to

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

Hi Sara, 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 delete

Re: [Avogadro-Discuss] Avogadro 2 0.7.0 Released

On Tue, Dec 3, 2013 at 11:14 AM, Stephen P. Molnar s.mol...@sbcglobal.netwrote: Thank you for your note. I tried all of the force fields on cyclohexane with no change in the structure. Bear in mind that the conformer resulting from a computational geometry optimization depends heavily on the

Re: [Avogadro-Discuss] Output/Viewable/Zoom question

I'm not aware of a way to do this directly in avogadro, but exporting to svg / ps / pdf or some other vector graphics format will produce a resizeable image, which could then be rasterized to higher resolution raster image using something like imagemagick. Hope this helps, Dave On Sat, Jun 13,

Re: [Avogadro-Discuss] XTALOPT hangs if server connection lost

On Fri, Aug 14, 2015 at 4:35 PM, Cohen, Ronald rco...@carnegiescience.edu wrote: I had fixed this in an earlier version but don't remember how. Sometimes the connection to the server or nameserver goes down (about once a day) and I see an error like: SSHConnectionLibSSH::isConnected():

Re: [Avogadro-Discuss] xtalopt not digesting pwscf (quantum espresso) output

On Thu, Jul 30, 2015 at 8:46 AM, Ronald Cohen rco...@carnegiescience.edu wrote: I can try to fix myself. Will let you know. Thanks! Ron That's be awesome! I'm away from my main development computer at the moment, so you can probably get to it faster than me :) The parsing code is in the

Re: [Avogadro-Discuss] Regarding the execution of gamess input file

This looks like an issue with GAMESS itself. I'd suggest contacting them as they'll be able to better help you. Dave On Tue, Mar 22, 2016 at 5:43 AM, Rajat Gupta wrote: > Dear sir, > > I am generating an input file for the calculation of energy of a cluster > for gamess

Re: [Avogadro-Discuss] Yaehmop Additions

Very cool -- this is a nice addition for crystallographers! On Sun, Sep 4, 2016 at 11:13 PM, Patrick Avery wrote: > Hello Avogadro community! > > I've been working on implementing some extended Huckel theory calculations > into Avogadro through YAeHMOP. It's pretty exciting

Re: [Avogadro-Discuss] [Avogadro-devel] GSoC 2016

On Sun, Sep 11, 2016 at 9:26 PM, Patrick Avery wrote: > Hey Avogadro community! > > Just wanted to provide an update for GSoC. I was fortunately able to pass! > > I added a lot of features to Avogadro 2 that will probably be helpful for > materials science groups. Here is a