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 something I have wanted to add to Avogadro in a more formal way, but there is only so much time in a day. I am not aware of an extension targeted to this area as yet. Please speak up if anyone out there has more information I am missing. Best, Marcus -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
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) but this isn't present in the Ubuntu Avogadro version. In the latter the Extensions drop down does not have Molecular Mechanics. Both are Avogadro 1.1.1. Can any suggest a remedy for my problem? This is odd, is the Ubuntu version built by you or packaged by Ubuntu? I have Ubuntu 14.04, and so can take a look on there if you give me a little more detail. These extensions are provided by Open Babel, you may need to install more pieces of Open Babel. Thanks, Marcus -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
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 Fri, Apr 17, 2015 at 9:19 AM, Cohen, Ronald rco...@carnegiescience.edu wrote: It runs fine under nomachine, but the enterprise version of nomachine needed to have virtual desktops is very expensive. Thanks, Ron --- Ronald Cohen Geophysical Laboratory Carnegie Institution 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 rco...@carnegiescience.edu office: 202-478-8937 skype: ronaldcohen https://twitter.com/recohen3 https://www.linkedin.com/profile/view?id=163327727 On Thu, Apr 16, 2015 at 11:56 PM, Cohen, Ronald rco...@carnegiescience.edu wrote: This is driving me crazy, and maybe someone has seen it. I have tried everything. I have a new ubuntu 14 machine and I built everthing with no errors, and avogadro runs fine on the console and ssh -X , but when I try to run it under vnc it always crashes the X server. I have tried every xserver I could find and every version of xstartup I could find. The whole vnc client crashes when I try just avogadro. After a crash the vnc log file shows: Thu Apr 16 23:46:04 2015 Connections: accepted: 0.0.0.0::51330 SConnection: Client needs protocol version 3.8 SConnection: Client requests security type VncAuth(2) VNCSConnST: Server default pixel format depth 16 (16bpp) little-endian rgb565 VNCSConnST: Client pixel format depth 16 (16bpp) little-endian rgb565 XIO: fatal IO error 11 (Resource temporarily unavailable) on X server :16 after 172 requests (172 known processed) with 0 events remaining. If I run avogadro -h under vnc I see (and it does not crash the server): avogadro -h Xlib: extension XInputExtension missing on display :16. Avogadro version: 1.1.1 Git: 5e4d1f7 LibAvogadro version: 1.1.1 Git: 5e4d1f7 Locale: en_GB Translation successfully loaded. Usage: avogadro [options] [files] Avogadro - Advanced Molecular Editor (version 1.1.1) Options: -h, --help Show help options (this) -v, --version Show version information So there are too symptoms--the XIO crash and the Xlib: extension XInputExtension missing on display :16. Neither of these happen on the console or a regular sh -X session. I really need to get this working under vnc, so if anyone has any ideas or experience with this I would greatly appreciate it! Thank you! Sincerely, Ron --- Ronald Cohen Geophysical Laboratory Carnegie Institution 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 rco...@carnegiescience.edu office: 202-478-8937 skype: ronaldcohen https://twitter.com/recohen3 https://www.linkedin.com/profile/view?id=163327727 -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
Re: [Avogadro-Discuss] avogadro crashes X on ubuntu 14 under vnc
I have tried everything, but mainly vnc4server and tightvncserver as servers, and jollysfastvnc as the client. Note however it seems that X server crashes, not just VNC and not the client. Even with a bug it seems only the program should crash, not everything. I found it works fine with NX (nomachine), but that is expensive. It is completely reproducible--it never works under regular vnc. Ron --- Ronald Cohen Geophysical Laboratory Carnegie Institution 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 rco...@carnegiescience.edu office: 202-478-8937 skype: ronaldcohen https://twitter.com/recohen3 https://www.linkedin.com/profile/view?id=163327727 On Mon, Apr 20, 2015 at 3:49 PM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: 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 Fri, Apr 17, 2015 at 9:19 AM, Cohen, Ronald rco...@carnegiescience.edu wrote: It runs fine under nomachine, but the enterprise version of nomachine needed to have virtual desktops is very expensive. Thanks, Ron --- Ronald Cohen Geophysical Laboratory Carnegie Institution 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 rco...@carnegiescience.edu office: 202-478-8937 skype: ronaldcohen https://twitter.com/recohen3 https://www.linkedin.com/profile/view?id=163327727 On Thu, Apr 16, 2015 at 11:56 PM, Cohen, Ronald rco...@carnegiescience.edu wrote: This is driving me crazy, and maybe someone has seen it. I have tried everything. I have a new ubuntu 14 machine and I built everthing with no errors, and avogadro runs fine on the console and ssh -X , but when I try to run it under vnc it always crashes the X server. I have tried every xserver I could find and every version of xstartup I could find. The whole vnc client crashes when I try just avogadro. After a crash the vnc log file shows: Thu Apr 16 23:46:04 2015 Connections: accepted: 0.0.0.0::51330 SConnection: Client needs protocol version 3.8 SConnection: Client requests security type VncAuth(2) VNCSConnST: Server default pixel format depth 16 (16bpp) little-endian rgb565 VNCSConnST: Client pixel format depth 16 (16bpp) little-endian rgb565 XIO: fatal IO error 11 (Resource temporarily unavailable) on X server :16 after 172 requests (172 known processed) with 0 events remaining. If I run avogadro -h under vnc I see (and it does not crash the server): avogadro -h Xlib: extension XInputExtension missing on display :16. Avogadro version: 1.1.1 Git: 5e4d1f7 LibAvogadro version: 1.1.1 Git: 5e4d1f7 Locale: en_GB Translation successfully loaded. Usage: avogadro [options] [files] Avogadro - Advanced Molecular Editor (version 1.1.1) Options: -h, --help Show help options (this) -v, --version Show version information So there are too symptoms--the XIO crash and the Xlib: extension XInputExtension missing on display :16. Neither of these happen on the console or a regular sh -X session. I really need to get this working under vnc, so if anyone has any ideas or experience with this I would greatly appreciate it! Thank you! Sincerely, Ron --- Ronald Cohen Geophysical Laboratory Carnegie Institution 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 rco...@carnegiescience.edu office: 202-478-8937 skype: ronaldcohen https://twitter.com/recohen3 https://www.linkedin.com/profile/view?id=163327727 -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop