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Showing results of 1260

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 [Avogadro-Discuss] question about germanene nanoribbon From: Azadeh Ayatollahie - 2017-05-24 15:09:22 Attachments: Message as HTML Dear all I need 7-AGeNR( Armchair germanene nanoribbon) input file in siesta(7-AGeNR.fdf). I will be so grateful if you send it to me or tell me how I can find it. best regards Azadeh 
 [Avogadro-Discuss] (no subject) From: Azadeh Ayatollahie - 2017-05-24 05:41:27 Attachments: Message as HTML
 [Avogadro-Discuss] question about germanene nanoribbon From: Azadeh Ayatollahie - 2017-05-23 04:43:35 Attachments: Message as HTML Dear all I need 7-AGeNR( Armchair germanene nanoribbon) input file in siesta(7-AGeNR.fdf). I will be so grateful if you send it to me or tell me how I can find it. best regards Azadeh 
 [Avogadro-Discuss] question about germanene nanoribbon From: Azadeh Ayatollahie - 2017-05-12 16:48:31 Attachments: Message as HTML Dear all I need 7-AGeNR( Armchair germanene nanoribbon) input file in siesta(7-AGeNR.fdf). I will be so grateful if you send it to me or tell me how I can find it. best regards Azadeh 
 Re: [Avogadro-Discuss] Avogradro installation problem (Linux) From: Hülsmann, Marco - 2017-05-02 11:42:41 Attachments: Message as HTML Hi Geoff, thanks for your replied. I tried the new version together with Eigen 3. Then, using cmake, I get /usr/local/hpc5/include_eigen/include/eigen3" does not appear to contain CMakeLists.txt Why does it have to it contain it? In fact, it doesn't. Best regards, Marco Von: Geoffrey Hutchison [mailto:geoff.hutchison@...] Gesendet: Montag, 1. Mai 2017 21:36 An: avogadro-discuss@... Betreff: Re: [Avogadro-Discuss] Avogradro installation problem (Linux) One way or another, I think you are picking up Eigen 3. My suggestion would be to compile from the current Git version, that will become 1.3: https://github.com/cryos/avogadro Best regards, -Geoff 
 Re: [Avogadro-Discuss] Avogradro installation problem (Linux) From: Geoffrey Hutchison - 2017-05-01 19:35:43 Attachments: Message as HTML One way or another, I think you are picking up Eigen 3. My suggestion would be to compile from the current Git version, that will become 1.3: https://github.com/cryos/avogadro ; Best regards, -Geoff
 [Avogadro-Discuss] Avogradro installation problem (Linux) From: Hülsmann, Marco - 2017-04-28 16:16:51 Attachments: Avogadro_Error_Message.pdf Message as HTML Hello! I have problems with the installation of Avogadro on a Linux system. I installed OpenBabel and Eigen2 successfully and used cmake with the options -DEIGEN2_INCLUDE_DIR, -DOPENBABEL2_INCLUDE_DIR and -DOPENBABEL2_LIBRARIES (I indicated the libinchi.so). The OpenBabel version is 2.3.2. When I type "make", I get some curious C++ error messages (see attachment). They are in German. In English, it would be "Error: >> Transform3d<< in namespace >>Eigen<< does not denote a type Const Eigen::Transform3d & modelview() const;" Does anybody know about this problem? I'm looking forward to any helpful reply! Thank you very much in advance! Marco --- Dr. rer. nat. Marco Hülsmann (Dipl.-Math.) Fachbereich Informatik & Fachbereich für Elektrotechnik, Maschinenbau und Technikjournalismus (EMT) Hochschule Bonn-Rhein-Sieg Grantham-Allee 20 53757 Sankt Augustin Raum B-112 Tel.: 02241/865-391 
 Re: [Avogadro-Discuss] UNL after using Fill Unit Cell From: Željko M. Svedružić - 2017-04-24 16:00:19 Attachments: Message as HTML  Hi, we are preparing our compounds in Avogadro 1.1.1.1 and then use them in Gromacs and NAMD. We save the compounds as mol2 file in Avogadro, than we import the mol2 file to some parametrization program such as AcPype. AcPype will give you a PDF format for the ligand that you can stick at the end of your PDB file with protein coordinates. The PDB can be tan converted to gmx with pdb2gmx or to psf with VMD psf builder. Hope this helps, it works for us great in the last two years Cheers, http://www.svedruziclab.com On 2017-04-23 10:12, Nash, Anthony wrote: > Hi all, > > I am trying to recreate the unit cell assemblage of 4z1r (visible using the PDB NGL viewer on the website). > > After importing my structure and checking the unit cell dimensions, I set the space group (5 c 2y c 1 2 1 as determined using Maestro) then select "Fill Unit Cell". Visually, everything looks good. But unfortunately, all means of identifying the atom and the corresponding residue is lost in the exported pdb and matching/replicated atoms as listed together rather than in their corresponding residue order. I plan on importing this into Gromacs, but in its current state the .pdb file is impossible to read. > > E.g., > > HETATM 1 N UNL 1 3.631 3.685 8.676 1.00 0.00 N > > HETATM 2 N UNL 2 165.943 3.685 16.225 1.00 0.00 N > > HETATM 3 N UNL 3 89.418 10.655 8.676 1.00 0.00 N > > HETATM 4 N UNL 4 80.156 10.655 16.225 1.00 0.00 N > > HETATM 5 C UNL 5 4.854 4.502 8.763 1.00 0.00 C > > HETATM 6 C UNL 6 164.720 4.502 16.138 1.00 0.00 C > > HETATM 7 C UNL 7 90.640 11.472 8.763 1.00 0.00 C > > HETATM 8 C UNL 8 78.933 11.472 16.138 1.00 0.00 C > > HETATM 9 C UNL 9 6.049 3.864 8.047 1.00 0.00 C > > HETATM 10 C UNL 10 163.525 3.864 16.854 1.00 0.00 C > > HETATM 11 C UNL 11 91.836 10.833 8.047 1.00 0.00 C > > HETATM 12 C UNL 12 77.738 10.833 16.854 1.00 0.00 C > > HETATM 13 O HOH 13 5.956 2.719 7.616 1.00 0.00 O > > HETATM 14 O HOH 14 163.618 2.719 17.285 1.00 0.00 O > > HETATM 15 O HOH 15 91.743 9.688 7.616 1.00 0.00 O > > HETATM 16 O HOH 16 77.831 9.688 17.285 1.00 0.00 O > > Any idea how to fix this? > > I'm beginning to think the only way around this would be to import my asymmetric unit structure into Gromacs, replicate the protein, identify the x,y,z location of a central atom from within Avogadro of one of the three replicated molecules, and perform some basic maths to translate the copies. > > Thanks > Anthony > > Dr Anthony Nash > Department of Chemistry > University College London > > _SKELETAL TISSUE DYNAMICS GROUP_ > _COMMITTEE MEMBER OF LONDON MATRIX GROUP _@... -- **************address file******************* Željko Svedružić Ph.D. zsvedruz@... web: https://profiles.google.com/106720515809875304148#106720515809875304148/about ************************************************** 
 Re: [Avogadro-Discuss] UNL after using Fill Unit Cell From: Geoffrey Hutchison - 2017-04-24 15:22:11 Attachments: Message as HTML > After importing my structure and checking the unit cell dimensions, I set the space group (5 c 2y c 1 2 1 as determined using Maestro) then select “Fill Unit Cell”. Visually, everything looks good. But unfortunately, all means of identifying the atom and the corresponding residue is lost in the exported pdb and The problem is that the "fill unit cell" does not necessarily match bonds and bond orders from the molecule. Consequently, when saving to PDB, the code attempts to perceive residues and can't match any of them (e.g., C-O instead of C=O for all amino acids). While in your case, it might be reasonable to copy bond orders, in the general case, this is impossible since bonds can go across unit cell boundaries. I don't know if Pymol will do this, but that would be my current suggestion- it has much better feature support for biomolecules. Hope that helps, -Geoff
 [Avogadro-Discuss] UNL after using Fill Unit Cell From: Nash, Anthony - 2017-04-23 08:12:14 Attachments: Message as HTML Hi all, I am trying to recreate the unit cell assemblage of 4z1r (visible using the PDB NGL viewer on the website). After importing my structure and checking the unit cell dimensions, I set the space group (5 c 2y c 1 2 1 as determined using Maestro) then select “Fill Unit Cell”. Visually, everything looks good. But unfortunately, all means of identifying the atom and the corresponding residue is lost in the exported pdb and matching/replicated atoms as listed together rather than in their corresponding residue order. I plan on importing this into Gromacs, but in its current state the .pdb file is impossible to read. E.g., HETATM 1 N UNL 1 3.631 3.685 8.676 1.00 0.00 N HETATM 2 N UNL 2 165.943 3.685 16.225 1.00 0.00 N HETATM 3 N UNL 3 89.418 10.655 8.676 1.00 0.00 N HETATM 4 N UNL 4 80.156 10.655 16.225 1.00 0.00 N HETATM 5 C UNL 5 4.854 4.502 8.763 1.00 0.00 C HETATM 6 C UNL 6 164.720 4.502 16.138 1.00 0.00 C HETATM 7 C UNL 7 90.640 11.472 8.763 1.00 0.00 C HETATM 8 C UNL 8 78.933 11.472 16.138 1.00 0.00 C HETATM 9 C UNL 9 6.049 3.864 8.047 1.00 0.00 C HETATM 10 C UNL 10 163.525 3.864 16.854 1.00 0.00 C HETATM 11 C UNL 11 91.836 10.833 8.047 1.00 0.00 C HETATM 12 C UNL 12 77.738 10.833 16.854 1.00 0.00 C HETATM 13 O HOH 13 5.956 2.719 7.616 1.00 0.00 O HETATM 14 O HOH 14 163.618 2.719 17.285 1.00 0.00 O HETATM 15 O HOH 15 91.743 9.688 7.616 1.00 0.00 O HETATM 16 O HOH 16 77.831 9.688 17.285 1.00 0.00 O Any idea how to fix this? I’m beginning to think the only way around this would be to import my asymmetric unit structure into Gromacs, replicate the protein, identify the x,y,z location of a central atom from within Avogadro of one of the three replicated molecules, and perform some basic maths to translate the copies. Thanks Anthony Dr Anthony Nash Department of Chemistry University College London Skeletal Tissue Dynamics Group Committee member of London Matrix Group @LondonMatrixGrp 
 Re: [Avogadro-Discuss] GSoC person to contact in regard to Molecular Dynamics project in Avogadro2 From: Marcus D. Hanwell - 2017-03-28 14:21:01 On Tue, Mar 28, 2017 at 2:34 AM, Piyush Divyankar wrote: > > hello, > I wish to know who should I approach to learn more about the molecular dynamics project in Avogadro2. > That would be me, the projects all have mentors with email addresses, e.g. http://wiki.openchemistry.org/GSoC_Ideas_2017#Project:_Molecular_Dynamics for this one. Feel free to discuss your ideas on the list, I am sure Geoff will be interested in this too. Marcus 
 [Avogadro-Discuss] GSoC person to contact in regard to Molecular Dynamics project in Avogadro2 From: Piyush Divyankar - 2017-03-28 06:34:59 Attachments: Message as HTML hello, I wish to know who should I approach to learn more about the molecular dynamics project in Avogadro2. Piyush Divyankar Graduate Metallurgical Engineering and Material Sciences IIT Bombay 
 [Avogadro-Discuss] Want to Support Avogadro? From: Geoffrey Hutchison - 2017-03-24 17:42:17 Dear Avogadro community, A while ago, I circulated a survey about financial support for Avogadro. The results were very positive - lots of people were willing and interested in contributing to fund Avogadro development and promotion. I talked a bit with Marcus and investigated several options. My biggest concern is that Avogadro has always been about an open community. So I'm pleased to announce that Avogadro is now part of an Open Collective: https://opencollective.com/avogadro Open Collective provides a transparent, sustainable, and secure way for people to support and sponsor open source projects, including webpack, Yeoman, and hundreds of other open source projects. What makes it different, is that anyone can request reimbursement - and both budget and all expenses will be transparent. • Open involvement for anyone • Both individuals and companies can sponsor, fund, or back us (with potential tax benefits). • Following the money is easy and open • You help decide the future of Avogadro through your support • Anyone can collect funds by contributing to Avogadro While the default is for a monthly contribution, you can contribute yearly or one-time. What are we going to do with the funds? • Documentation and tutorials - the University of Pittsburgh has funded our manual (https://avogadro.cc/docs/) but we'd like to add more educational materials and tutorials • Bounties - I recently funded a "bounty" to enable Avogadro 1.3 to use the Eigen 3.x matrix library and we'd like to fund other bug fixes and feature requests • Publicity - I have ordered Avogadro stickers to distribute at the upcoming ACS meeting in San Francisco. We want to "get the word out" for both users and contributors • Your idea here - we'd like new ideas and input - what does Avogadro need most? This will never become a for-profit project, but we believe that using Open Collective and your support, we can attract new contributions and sustain all levels of Avogadro development and support. Thoughts? Suggestions? -Geoff 
 [Avogadro-Discuss] question about the expected behaviour of "Label" From: Davide Olianas - 2017-02-14 14:01:15 Attachments: Message as HTML Hello everyone, I opened an Issue ; on github because I though I found a bug. The issue was quickly closed because “the labels won’t show if the atoms are too far from the camera”. I may be misinterpreting the meaning of the sentence because English isn’t my first language, but the labels appear to be working in a bizarre way on my machine. If the labels show from the beginning (i.e when opening the file), they still show no matter how much I zoom out; on the other hand, if the labels don’t show from the beginning, they don’t appear no matter how much I zoom in. Please see the attached images from the third comment on github. Can someone illuminate me? Thanks, Davide ​ 
 [Avogadro-Discuss] New Website From: Geoffrey Hutchison - 2017-02-10 17:32:56 I'd like to announce a new Avogadro website (http://avogadro.cc/) built with the Jekyll static site generator (from http://github.com/avogadro/avogadro.cc) The new site is responsive for mobile/tablet use, and should generally load faster - particularly when revisiting pages. Features: - Full manual (from http://manual.avogadro.cc -> https://avogadro.cc/docs/) - It's still editable - there is a link at the bottom of all pages that allows anyone to edit via GitHub - It's translatable - it's a set of Markdown files and we can produce multiple languages and localizations - No cookies or user tracking - Share buttons on all pages - Embedded comments via http://discuss.avogadro.cc (Right now, this is enabled for news posts, but I can open it up to other sections easily.) - Author profiles - if you add content, you can have a sidebar profile for attribution - Embedded MathJax - Embedding videos from YouTube and Vimeo It's not perfect. If you have comments, concerns, etc. please comment here or submit an issue: https://github.com/avogadro/avogadro.cc/issues For now, old content is still available - let me know if I missed something. Thanks, -Geoff 
 Re: [Avogadro-Discuss] Avogadro Crash while reading an output file. From: Geoffrey Hutchison - 2017-01-31 19:27:21 > Avogadro is a wonderful program, we love it, just sometimes with it needs some help from VMD and wxMacMolPlt :-) Certainly packages like GAMESS have their own “native” programs like wxMacMolPlt. There’s no way that Avogadro could replace those (e.g., GaussView, IQMol, etc.) Moreover, we have no interest in replacing VMD or PyMol - both are great programs. Avogadro aims to be the best “builder” possible, and obviously that includes reading output files. I appreciate when we get crash reports, and I think this is now fixed. I’m also working on a broader solution with a crash-reporting system like Firefox or Chrome. -Geoff 
 Re: [Avogadro-Discuss] Avogadro Crash while reading an output file. From: Željko M. Svedružić - 2017-01-30 20:42:07 Attachments: text/plain  Avogadro is a wonderful program, we love it, just sometimes with it needs some help from VMD and wxMacMolPlt :-) On 2017-01-30 16:53, tim hockswender wrote: > Thanks much for the input. I also see that wxMacMolPlt [I'm on WIN10] reads the file with no issues. > Avogadro starts by saying 'reading multi-molecule file' which is clearly incorrect. > My need for Avogadro stems primarily from wanting to visualize NMR plots, from GAMESS output. I have also used the free WebMO program but it has bugs when calculating the NMR output versus a TMS reference. > Regards, > Tim > > On Sat, Jan 28, 2017 at 4:55 PM, Željko M. Svedružić wrote: > >> dear Tim, I can open your log file in MacMolPlt and see all the frequencies. No problems. I always use MacMolPlt with GAMESS output, Avogadro is no reliable for GAMESS outputs even when it apparently reads the file. >> >> On 2017-01-09 20:32, tim hockswender wrote: >> >>> Attempting to open the attached log file leads to a crash every time. >>> "Avogadro has stopped working" >>> Inspecting the log file shows no compute errors, just 'chemical error of un-optimized PES >>> I have latest Avogadro (see image attached) and using GAMESS R2013. >>> [Making sure all is OK with GAMESS before using the new version.] >>> >>> Also attaching the inp file. >>> >>> Any advice? >>> Tom >> >> -- >> **************address file******************* >> Željko Svedružić Ph.D. >> zsvedruz@... >> web: >> https://profiles.google.com/106720515809875304148#106720515809875304148/about >> ************************************************** >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, SlashDot.org! http://sdm.link/slashdot [1] >> _______________________________________________ >> Avogadro-Discuss mailing list >> Avogadro-Discuss@... [2] >> https://lists.sourceforge.net/lists/listinfo/avogadro-discuss [3] -- **************address file******************* Željko Svedružić Ph.D. zsvedruz@... web: https://profiles.google.com/106720515809875304148#106720515809875304148/about ************************************************** Links: ------ [1] http://sdm.link/slashdot [2] mailto:Avogadro-Discuss@... [3] https://lists.sourceforge.net/lists/listinfo/avogadro-discuss [4] mailto:zsvedruz@... 
 Re: [Avogadro-Discuss] Avogadro Crash while reading an output file. From: tim hockswender - 2017-01-30 15:53:20 Attachments: image.png Message as HTML Thanks much for the input. I also see that wxMacMolPlt [I'm on WIN10] reads the file with no issues. Avogadro starts by saying 'reading multi-molecule file' which is clearly incorrect. My need for Avogadro stems primarily from wanting to visualize NMR plots, from GAMESS output. I have also used the free WebMO program but it has bugs when calculating the NMR output versus a TMS reference. Regards, Tim On Sat, Jan 28, 2017 at 4:55 PM, Željko M. Svedružić wrote: > dear Tim, I can open your log file in MacMolPlt and see all the > frequencies. No problems. I always use MacMolPlt with GAMESS output, > Avogadro is no reliable for GAMESS outputs even when it apparently reads > the file. > > > > On 2017-01-09 20:32, tim hockswender wrote: > > Attempting to open the attached log file leads to a crash every time. > "Avogadro has stopped working" > Inspecting the log file shows no compute errors, just 'chemical error of > un-optimized PES > I have latest Avogadro (see image attached) and using GAMESS R2013. > [Making sure all is OK with GAMESS before using the new version.] > > Also attaching the inp file. > > Any advice? > Tom > [image: Inline image 1] > > > > -- > **************address file******************* > Željko Svedružić Ph.D.zsvedruz@... > web:https://profiles.google.com/106720515809875304148#106720515809875304148/about > ************************************************** > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > Avogadro-Discuss mailing list > Avogadro-Discuss@... > https://lists.sourceforge.net/lists/listinfo/avogadro-discuss > > 
 Re: [Avogadro-Discuss] Avogadro Crash while reading an output file. From: Željko M. Svedružić - 2017-01-28 22:20:17 Attachments: text/plain  dear Tim, I can open your log file in MacMolPlt and see all the frequencies. No problems. I always use MacMolPlt with GAMESS output, Avogadro is no reliable for GAMESS outputs even when it apparently reads the file. On 2017-01-09 20:32, tim hockswender wrote: > Attempting to open the attached log file leads to a crash every time. > "Avogadro has stopped working" > Inspecting the log file shows no compute errors, just 'chemical error of un-optimized PES > I have latest Avogadro (see image attached) and using GAMESS R2013. > [Making sure all is OK with GAMESS before using the new version.] > > Also attaching the inp file. > > Any advice? > Tom -- **************address file******************* Željko Svedružić Ph.D. zsvedruz@... web: https://profiles.google.com/106720515809875304148#106720515809875304148/about ************************************************** 
 Re: [Avogadro-Discuss] Avogadro Crash while reading an output file. From: Geoffrey Hutchison - 2017-01-28 21:37:44 Sorry this took a while to get to. The crash is caused by Open Babel - the GAMESS file format changed in reading vibrations. I have a patch or can point you at a Git version if that would help. What platform do you use for Avogadro? Thanks, -Geoff 
 [Avogadro-Discuss] freeze upon start - but for one user only From: Stanislav Šimko - 2017-01-24 17:22:26 Dear Avogadro developers and users, I'm facing freezes of Avogadro right upon starting it, both from terminal as well as gui. Unfortunately, I get only this error message: QStackedLayout::setCurrentWidget: Widget 0x55b28630e580 not contained in stack The thing is, that I can start it properly from either root account of from newly created user account (i.e. under my standard login I change user in terminal by "su foo").  I tried to remove \$HOME/.avogadro folder as well as some Qt folders to reset settings, but no changes. Do you please somebody have got any idea what could be wrong/how to debug the problem? Thank you. stanislav. 
 Re: [Avogadro-Discuss] Issue with Eigen3/avogadro1.1 From: Geoffrey Hutchison - 2017-01-13 18:42:52 Attachments: Message as HTML > #error Eigen2-support is only available up to version 3.2. Please go to > "http://eigen.tuxfamily.org/index.php?title=Eigen2"; We're well aware. (https://github.com/cryos/avogadro/issues/842 ;) Debian has a patch in their repository for avogadro-1.2: https://packages.debian.org/source/sid/avogadro ; I have posted a bounty on this issue as well: https://www.bountysource.com/issues/40246464-fails-to-buils-with-eigen-3-3 ; My hope is this can be fixed for a final avogadro-1.3 release. Hope that helps, -Geoff
 [Avogadro-Discuss] Issue with Eigen3/avogadro1.1 From: Javier Cerezo - 2017-01-13 17:17:22 Hello First of all, I want to thank the avogadro team for bringing such a nice code as an open source project. I am compiling version 1.1 from git using Eigen3.3 (which seem to be the version in the latest ubuntu-like and arch-like distros). cmake tests pass without any warning, but then I get an error in compilation time: #error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2"; This can be solved downgrading Eigen (I actually used Eigen2 to make it work). However, I would like to point that issue to the developers (or maybe it can be solved in any other way I am not aware of). Javier 
 [Avogadro-Discuss] Avogadro Crash while reading an output file. From: tim hockswender - 2017-01-09 19:33:03 Attachments: new1.log new1.inp image.png Message as HTML Attempting to open the attached log file leads to a crash every time. "Avogadro has stopped working" Inspecting the log file shows no compute errors, just 'chemical error of un-optimized PES I have latest Avogadro (see image attached) and using GAMESS R2013. [Making sure all is OK with GAMESS before using the new version.] Also attaching the inp file. Any advice? Tom [image: Inline image 1] 
 Re: [Avogadro-Discuss] [Avogadro-devel] Workflow Scripts (for Avo2) From: Geoffrey Hutchison - 2016-12-28 20:33:55 Attachments: Message as HTML > Have you looked at pymatgen? It has a lot of useful features for crystal structures and some also for molecules as well. Great idea. The pieces aren't fully in place, but there will be a system for workflow plugins to require dependencies. Do you have any first use cases, e.g., "insert structure from pymatgen"? Thanks, -Geoff 
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