On Tue, Mar 13, 2012 at 12:26 PM, David Lonie <lonieda...@gmail.com> wrote: > 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. > I would agree with David here. There are several command line components that have things like the underlying forcefields used in the GUI, Python bindings can make it easy to script them too. We never developed a powerful command line mode for Avogadro, because everything is in a library I think our efforts would be best focused in developing a command line frontend if it was useful, rather than trying to make the gui do both.
I am having trouble understanding how you are using Avogadro in a non-graphical context. Marcus ------------------------------------------------------------------------------ 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
