Hello David,
I thought since avogadro has python extension we can write scripts in
python and run them. I tried to execute a python script like that but the
problem is I cant turn off the graphics in avogadro. I will look into
openbabel and see if it does everything we need.
Thank you,
Divya
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.
>
> 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/
> >> _______________________________________________
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> >> 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
> >
>
--
Thanks
Divya
------------------------------------------------------------------------------
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/
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