Hi,
Hello Marcus, the problem we are facing is that we need to run scripts on
many molecules and we thought writing a script in python which would loop
through all the molecules would really help us but what happened is we
installed avogadro on a machine which cant bring up the graphic mode i.e.,
if we try to trigger the graphics the execution stops there. We installed
avogadro on that machine because it has computational power which is
require to perform our calculations. Openbabel supports some operations we
want. But I am not sure if openbabel will suffice all our requirements.
hello ray, thank you. I performed minimization using openbabel and it
worked for me. I will contact jing-yuan about it and see if openbabel would
meet our requirements.
Thank you very much for for your support.
Thank you,
Divya
On Tue, Mar 13, 2012 at 1:11 PM, Ray Sheppard <rshep...@iu.edu> wrote:
> Hi Divya,
> OpenBabel became part of your environment when you added the
> Avogadro SoftEnv key I sent to you. We use PBS (Torque actually)
> with a Maui Scheduler on top. It is much easier than Big Red's
> LoadLeveler.
> You can add "-I" to your qsub command. When your job starts, you
> have an interactive connection to the cluster where you can launch a
> remote X11
> session. More on Quarry's PBS is here: http://kb.iu.edu/data/avmy.html
> More on Remote X11 in general is here: http://kb.iu.edu/data/adhh.html
> and on Quarry specifically is here: http://kb.iu.edu/data/ahgh.html
> I'll hush again while y'all discuss what y'all do and how you do it.
> Ray
>
>
>
> On 3/13/2012 12:42 PM, Divya Neelagiri wrote:
>
> 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/
>> >> _______________________________________________
>> >> 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
>> >
>>
>
>
>
> --
> 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/
_______________________________________________
Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel
