Hi Divya, On Tue, Mar 13, 2012 at 11:27 AM, Divya Neelagiri <divne...@umail.iu.edu> wrote: > I need avogadro to perform minimization and some other operations on > proteins.
I'm not sure how you would perform any operations without the GUI, as there is no real command line interface to Avogadro. I think your best bet is to use the openbabel utilities. For instance, obminimize will perform a geometry relaxation using the same forcefield implementations that Avogadro uses: http://openbabel.org/wiki/Obminimize There are quite a few others that may help with the other tasks you need: http://openbabel.org/wiki/Guides Another option that I use with our remote clusters is to forward an X connection over SSH by using the -X or -Y options to ssh. This will launch the avogadro GUI on your workstation, even though it's actually running on the remote cluster. Hope this helps, Dave > We installed avogadro on quarry which is a super computer at IU. > In quarry we cant see the interface (graphics), we can only work with the > scripts and commands. For other softwares like VMD for example have an > option specified of how to turn off the graphics eg., "vmd -dispdev eof > -exit". I was wondering if there was any such similar command for avogadro > because in quarry if we are not able to turn off graphics it wont execute. > It just quits. Please suggest me what to fo on this issue. > > Thank you, > Divya > > On Sun, Mar 11, 2012 at 7:36 PM, Ray Sheppard <rshep...@iu.edu> wrote: >> >> Hi Dave, Thorsten, >> Please meet Divya. Hi Divya. Divya is the researcher in the School of >> Pharmacology >> who is taking the lead in this project. I am just an old physicist that >> got pressed into >> supercomputer duty about 30 years ago and hasn't figured out how to escape >> yet :) >> Divya can explain what she was trying to do and the issues she is trying >> to overcome. >> Please just keep me in the loop in case I need to build, rebuild or modify >> something. >> I have a GAMESS-UK copy on the machine, but it is getting a bit old. I do >> not think we have >> GAMESS-US on this machine. It might be living on Big Red. Thanks guys >> for helping. >> Ray >> >> On 3/11/2012 1:20 PM, Thorsten Hoffmann wrote: >> >> Why not use Gamess (US)? Avogadro can create an inputfile for Gamess. >> Gamess (and cfour) run on clusters. >> sincerely, >> Thorsten >> >> On Fri, Mar 9, 2012 at 1:28 PM, Ray Sheppard <rshep...@indiana.edu> wrote: >> >> Hello Avogadro Development folks, >> I recently installed Avogadro on a supercomputer for the School of >> Pharmacology. >> These machines work within a batch job environment. I was asked: >> "can you please tell me the command to execute avogadro without >> graphics?" >> >> I don't think this is possible with Avogadro -- AFAIK we never >> anticipated a use case that wouldn't need the display. What do they >> need to do in avogadro without graphics? >> >> It may be possible to accomplish what they need with some of the >> openbabel command-line tools? See >> >> http://openbabel.org/wiki/Guides >> >> Hope this helps, >> >> Dave >> >> >> ------------------------------------------------------------------------------ >> Virtualization & Cloud Management Using Capacity Planning >> Cloud computing makes use of virtualization - but cloud computing >> also focuses on allowing computing to be delivered as a service. >> http://www.accelacomm.com/jaw/sfnl/114/51521223/ >> _______________________________________________ >> Avogadro-devel mailing list >> Avogadro-devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/avogadro-devel >> >> >> >> >> >> ------------------------------------------------------------------------------ >> Virtualization & Cloud Management Using Capacity Planning >> Cloud computing makes use of virtualization - but cloud computing >> also focuses on allowing computing to be delivered as a service. >> http://www.accelacomm.com/jaw/sfnl/114/51521223/ >> >> >> >> _______________________________________________ >> Avogadro-devel mailing list >> Avogadro-devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/avogadro-devel >> >> > > > > -- > Thanks > Divya > ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d _______________________________________________ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
